diff --git a/openawsem/functionTerms/__init__.py b/openawsem/functionTerms/__init__.py index 60abc895..ada9b692 100644 --- a/openawsem/functionTerms/__init__.py +++ b/openawsem/functionTerms/__init__.py @@ -4,4 +4,5 @@ from . import membraneTerms from . import biasTerms from . import templateTerms -from . import hydrogenBondTerms \ No newline at end of file +from . import hydrogenBondTerms +from . import constraints diff --git a/openawsem/functionTerms/basicTerms.py b/openawsem/functionTerms/basicTerms.py index af21a027..a76f749b 100644 --- a/openawsem/functionTerms/basicTerms.py +++ b/openawsem/functionTerms/basicTerms.py @@ -19,6 +19,14 @@ 'LEU':'L', 'LYS':'K', 'MET':'M', 'PHE':'F', 'PRO':'P', 'SER':'S', 'THR':'T', 'TRP':'W', 'TYR':'Y', 'VAL':'V'} +def find_chain_index(res: int, chain_starts, chain_ends) -> int: + """ + Find the index of the chain that contains the residue with index `res`. + """ + + chain_index = [int(chain_start<=res and res<=chain_end) for chain_start,chain_end in zip(chain_starts,chain_ends)] + assert sum(chain_index) == 1, f"res: {res}, chain_starts: {chain_starts}, chain_ends: {chain_ends}, list: {chain_index}" + return chain_index.index(1) def con_term(oa, k_con=50208, bond_lengths=[.3816, .240, .276, .153], forceGroup=20): # add con forces @@ -97,85 +105,88 @@ def chi_term(oa, k_chi=251.04, chi0=-0.71, forceGroup=20): chi.setForceGroup(forceGroup) return chi -def excl_term(oa, k_excl=8368, r_excl=0.35, excludeCB=False, forceGroup=20): +def excl_term(oa, k_excl=8368, excludeCB=False, forceGroup=20): # add excluded volume - # Still need to add element specific parameters # 8368 = 20 * 4.184 * 100 kJ/nm^2, converted from default value in LAMMPS AWSEM + # # multiply interaction strength by overall scaling - # Openawsem doesn't have the distance range (r_excl) change from 0.35 to 0.45 when the sequence separtation more than 5 k_excl *= oa.k_awsem - excl = CustomNonbondedForce(f"{k_excl}*step({r_excl}-r)*(r-{r_excl})^2") - - if oa.periodic_box: - excl.setNonbondedMethod(excl.CutoffPeriodic) - print('\nexcl_term is periodic') - else: - excl.setNonbondedMethod(excl.CutoffNonPeriodic) - - pos = oa.pdb.positions + # We want to exclude "bonded" atoms from the potential. + # The bonded real (non-virtual site) pairs are: + # CA_i - O_i + # CA_i - CB_i + # CA_i - CA_i+1 + # O_i - CA_i+1 + # CAs and Os are never added as InteractionGroups, + # so we don't need to worry about excluding CA-O bonds. + # Since CB-O pairs aren't added as InteractionGroups, either, + # we can knock out the same-residue CA-CB interaction without side effects + # simply by requiring both atoms to have different resIds. + same_allow = "(1-delta(resId1-resId2))" + # If resId1 and resId2 separation is 1 and both are CA + # and they're in the same chain, set interaction to 0 + diff1_allow = '(1-same_chain*delta(abs(resId1-resId2)-1)*isCA1*isCA2)' + # initialize Force + base_energy_string = f"{k_excl}*{same_allow}*{diff1_allow}*(close_in_sequence*step(rI-r)*((rI-r)^2)+(1-close_in_sequence)*step(rII-r)*((rII-r)^2))" + # we can't use openmm's ^^^^^^^^^^^^^^^^^^^^^^^^ automatic bonded exclusions because they have to be the same for all Forces, + # so we program the exclusion for adjacent (bonded) particles into the potential + definitions = ";rI=0.35\ + ;rII=max(r_preferred2,r_preferred1)\ + ;close_in_sequence=same_chain*(1-at_least_5)\ + ;at_least_5=step(abs(resId2-resId1)-5)\ + ;same_chain=delta(chainId2-chainId1)" + energy_string = f'{base_energy_string}{definitions}' + excl = CustomNonbondedForce(energy_string) + # set parameters and add particles + excl.addPerParticleParameter("chainId") + excl.addPerParticleParameter("resId") + excl.addPerParticleParameter("r_preferred") + excl.addPerParticleParameter("isCA") for i in range(oa.natoms): - excl.addParticle() + res = oa.resi[i] + if res != -1: + chain = find_chain_index(res, oa.chain_starts, oa.chain_ends) + else: # resi==-1 reserved for DNA residues that shouldn't be included + chain = -1 # dummy parameter for when we add the particle to the Force + # (all particles must be added to the Force, but non-protein + # particles won't interact with anything because they're not + # included in any InteractionGroups) + # VVVV change to 0.35 and tests will pass + excl.addParticle([chain, res, 0.45 if i not in oa.o else 0.35, 1 if i in oa.ca else 0]) + # set groups of interacting particles excl.addInteractionGroup(oa.ca, oa.ca) if not excludeCB: excl.addInteractionGroup([x for x in oa.cb if x > 0], [x for x in oa.cb if x > 0]) excl.addInteractionGroup(oa.ca, [x for x in oa.cb if x > 0]) excl.addInteractionGroup(oa.o, oa.o) - - excl.setCutoffDistance(r_excl) - excl.createExclusionsFromBonds(oa.bonds, 1) - excl.setForceGroup(forceGroup) - return excl - - -def excl_term_v2(oa, k_excl=8368, r_excl=0.35, periodic=False, excludeCB=False, forceGroup=20): - # this version remove the use of "createExclusionsFromBonds", which could potentially conflict with other CustomNonbondedForce and causing "All forces must have the same exclusion". - # add excluded volume - # Still need to add element specific parameters - # 8368 = 20 * 4.184 * 100 kJ/nm^2, converted from default value in LAMMPS AWSEM - # multiply interaction strength by overall scaling - # Openawsem doesn't have the distance range (r_excl) change from 0.35 to 0.45 when the sequence separtation more than 5 - k_excl *= oa.k_awsem - excl = CustomNonbondedForce(f"{k_excl}*step(abs(res1-res2)-2+isChainEdge1*isChainEdge2+isnot_Ca1+isnot_Ca2)*step({r_excl}-r)*(r-{r_excl})^2") - + # finalize and return Force + excl.setCutoffDistance(0.45) + #excl.createExclusionsFromBonds(oa.bonds, 1) if oa.periodic_box: excl.setNonbondedMethod(excl.CutoffPeriodic) - print("\nexcel_term is periodic") + print('\nexcl_term is periodic') else: excl.setNonbondedMethod(excl.CutoffNonPeriodic) - - excl.addPerParticleParameter("res") - excl.addPerParticleParameter("isChainEdge") - excl.addPerParticleParameter("isnot_Ca") - for i in range(oa.natoms): - # print(oa.resi[i]) - if (i in oa.chain_ends) or (i in oa.chain_starts): - # print(i) - isChainEdge = 1 - else: - isChainEdge = 0 - if (i in oa.ca): - isnot_Ca = 0 - else: - isnot_Ca = 1 - excl.addParticle([oa.resi[i], isChainEdge, isnot_Ca]) - # print(oa.ca) - # print(oa.bonds) - # print(oa.cb) - excl.addInteractionGroup(oa.ca, oa.ca) - if not excludeCB: - excl.addInteractionGroup([x for x in oa.cb if x > 0], [x for x in oa.cb if x > 0]) - excl.addInteractionGroup(oa.ca, [x for x in oa.cb if x > 0]) - excl.addInteractionGroup(oa.o, oa.o) - - excl.setCutoffDistance(r_excl) - - # excl.setNonbondedMethod(excl.CutoffNonPeriodic) - # print(oa.bonds) - # print(len(oa.bonds)) - # excl.createExclusionsFromBonds(oa.bonds, 1) excl.setForceGroup(forceGroup) return excl + +def excl_term_v2(oa, k_excl=8368, r_excl=0.35, periodic=False, excludeCB=False, forceGroup=20): + # This term modified the potential energy expression to account for bonded exclusions + # (setting the potential to 0 for bonded atoms). These modifications have now been + # integrated into excl_term, making excl_term_v2 redundant. This function remains + # only for backward compatibility. + # + # (Previously, excl_term used openmm's NonbondedForce.createExclusionsFromBonds(oa.bonds, 1) + # to exclude all pairs of directly bonded atoms, but this caused issues for protein-DNA + # systems because certain DNA or protein-DNA Forces required a different exclusion list, + # and openmm requires all Forces that implement exclusions to use the same list) + if r_excl != 0.35: + # r_excl should never have been made a parameter because it has, to my knowledge, + # never been adjusted + raise ValueError(f"r_excl must be 0.35 but was {r_excl}") + return excl_term(oa, k_excl=k_excl, excludeCB=excludeCB, forceGroup=forceGroup) + def rama_term(oa, k_rama=8.368, num_rama_wells=3, w=[1.3149, 1.32016, 1.0264], sigma=[15.398, 49.0521, 49.0954], omega_phi=[0.15, 0.25, 0.65], phi_i=[-1.74, -1.265, 1.041], omega_psi=[0.65, 0.45, 0.25], psi_i=[2.138, -0.318, 0.78], forceGroup=21): # add Rama potential # 8.368 = 2 * 4.184 kJ/mol, converted from default value in LAMMPS AWSEM diff --git a/openawsem/functionTerms/constraints.py b/openawsem/functionTerms/constraints.py index 8131c9db..f22e3cd3 100644 --- a/openawsem/functionTerms/constraints.py +++ b/openawsem/functionTerms/constraints.py @@ -19,7 +19,7 @@ def constraint_by_distance(oa, res1, res2, d0=0*angstrom, forceGroup=3, k=1*kil constraint.setForceGroup(forceGroup) return constraint -def group_constraint_by_distance(oa, d0=0*angstrom, group1=[oa.ca[0], oa.ca[1]], group2=[oa.ca[2], oa.ca[3]], forceGroup=3, k=1*kilocalorie_per_mole): +def group_constraint_by_distance(oa, d0=0*angstrom, group1=[0, 1], group2=[2, 3], forceGroup=3, k=1*kilocalorie_per_mole): # CustomCentroidBondForce only work with CUDA not OpenCL. # # note added 11 Jun 2025: CustomCentroidBondForce worked for me on OpenCL on my workstation, ws1808 diff --git a/openawsem/functionTerms/contactTerms.py b/openawsem/functionTerms/contactTerms.py index d05e733e..690c5747 100644 --- a/openawsem/functionTerms/contactTerms.py +++ b/openawsem/functionTerms/contactTerms.py @@ -66,9 +66,294 @@ def inSameChain(i,j,chain_starts,chain_ends): return same_chain -def contact_term(oa, k_contact=4.184, k_burial = None, z_dependent=False, z_m=1.5, inMembrane=False, membrane_center=0*angstrom, k_relative_mem=1.0, parametersLocation=None, burialPartOn=True, withExclusion=False, forceGroup=22, - gammaName="gamma.dat", burialGammaName="burial_gamma.dat", membraneGammaName="membrane_gamma.dat", r_min=0.45,min_sequence_separation=10,min_sequence_separation_mem=10, - direct_mask_ij=None, water_mask_ij=None, protein_mask_ij=None): +def contact_term_with_density_dependent_helical_HB( + oa, k_contact=4.184, k_burial = None, z_dependent=False, z_m=1.5, inMembrane=False, membrane_center=0*angstrom, k_relative_mem=1.0, parametersLocation=None, burialPartOn=True, withExclusion=False, forceGroup=22, + gammaName="gamma.dat", burialGammaName="burial_gamma.dat", membraneGammaName="membrane_gamma.dat", r_min=0.45,min_sequence_separation=10,min_sequence_separation_mem=10, + direct_mask_ij=None, water_mask_ij=None, protein_mask_ij=None, k_helical=4.184, helical_gamma_i=[0.77,0.68,0.07,0.15,0.23,0.33,0.27,0.0,0.06,0.23,0.62,0.65,0.50,0.41,-3.0,0.35,0.11,0.45,0.17,0.14]): + """ + THIS DOESN'T WORK BECAUSE THE CustomGBForce ONLY ALLOWS PAIRWISE + INTERACTIONS ONCE RHO IS CALCULATED, BUT CALCULATING THE REAL HB + FORCE REQUIRES AT LEAST 3 SITES PER BOND. WE CAN APPROXIMATE + WITH A PAIRWISE INTERACTION, BUT GENERALLY THE HELICAL RHO + CALCULATION HAS DIFFERENT PARAMETERS FOR THAT, SO WE HAVE A + DIFFERENT TERM FOR IT (hydrogenBondTerms.density_dependent_helical_term_approximate) + """ + raise NotImplementedError("this term doesn't work (see documentation)") + # helical_gamma_i is in ARND order because that's the order of gamma_se_map_1_letter + # set up masks to reweight contacts + if direct_mask_ij is not None and direct_mask_ij.shape != (oa.nres, oa.nres): + raise ValueError(f"direct_mask_ij should be of shape {(oa.nres, oa.nres)}, but got {direct_mask_ij.shape}") + if water_mask_ij is not None and water_mask_ij.shape != (oa.nres, oa.nres): + raise ValueError(f"water_mask_ij should be of shape {(oa.nres, oa.nres)}, but got {water_mask_ij.shape}") + if protein_mask_ij is not None and protein_mask_ij.shape != (oa.nres, oa.nres): + raise ValueError(f"protein_mask_ij should be of shape {(oa.nres, oa.nres)}, but got {protein_mask_ij.shape}") + # set up the rest of the parameters + if parametersLocation is None: + parametersLocation=openawsem.data_path.parameters + if isinstance(k_contact, float) or isinstance(k_contact, int): + k_contact = k_contact * oa.k_awsem # just for backward comptable + elif isinstance(k_contact, Quantity): + k_contact = k_contact.value_in_unit(kilojoule_per_mole) # convert to kilojoule_per_mole, openMM default uses kilojoule_per_mole as energy. + k_contact = k_contact * oa.k_awsem + else: + print(f"Unknown input, {k_contact}, {type(k_contact)}") + #setting burial + if k_burial == None: + k_burial = k_contact + elif isinstance(k_burial, float) or isinstance(k_burial, int): + k_burial = k_burial * oa.k_awsem # just for backward comptable + elif isinstance(k_burial, Quantity): + k_burial = k_burial.value_in_unit(kilojoule_per_mole) # convert to kilojoule_per_mole, openMM default uses kilojoule_per_mole as energy. + k_burial = k_burial * oa.k_awsem + else: + print(f"Unknown input, {k_burial}, {type(k_burial)}") + # combine direct, burial, mediated. + # default membrane thickness 1.5 nm + membrane_center = membrane_center.value_in_unit(nanometer) # convert to nm + + # r_min = .45 + r_max = .65 + r_minII = .65 + r_maxII = .95 + eta = 50 # eta actually has unit of nm^-1. + eta_sigma = 7.0 + rho_0 = 2.6 + #min_sequence_separation = 10 # means j-i > 9 we address this by passing in parameter + #min_sequence_separation_mem = 10 + nwell = 2 + eta_switching = 10 + gamma_ijm = np.zeros((nwell, 20, 20)) + water_gamma_ijm = np.zeros((nwell, 20, 20)) + protein_gamma_ijm = np.zeros((nwell, 20, 20)) + + # parameters for the sigma involved in the helical hbonds + helix_eta = 70 # see note on units for regular "eta" + helix_eta_sigma = 7.0 + helix_rho_0 = 3.0 + + # read in seq data. + seq = oa.seq + # read in gamma info + gamma_direct, gamma_mediated = read_gamma(os.path.join(parametersLocation, gammaName)) + + burial_kappa = 4.0 + burial_ro_min = [0.0, 3.0, 6.0] + burial_ro_max = [3.0, 6.0, 9.0] + burial_gamma = np.loadtxt(os.path.join(parametersLocation, burialGammaName)) + + k_relative_mem = k_relative_mem # adjust the relative strength of gamma + inMembrane = int(inMembrane) + contact = CustomGBForce() + + m = 0 # water environment + count = 0 + for i in range(20): + for j in range(i, 20): + gamma_ijm[m][i][j] = gamma_direct[count][0] + gamma_ijm[m][j][i] = gamma_direct[count][0] + count += 1 + count = 0 + for i in range(20): + for j in range(i, 20): + water_gamma_ijm[m][i][j] = gamma_mediated[count][1] + water_gamma_ijm[m][j][i] = gamma_mediated[count][1] + count += 1 + count = 0 + for i in range(20): + for j in range(i, 20): + protein_gamma_ijm[m][i][j] = gamma_mediated[count][0] + protein_gamma_ijm[m][j][i] = gamma_mediated[count][0] + count += 1 + # residue interaction table (step(abs(resId1-resId2)-min_sequence_separation)) + res_table = np.zeros((nwell, oa.nres, oa.nres)) + for i in range(oa.nres): + for j in range(oa.nres): + resId1 = i + resId2 = j + if abs(resId1-resId2)-min_sequence_separation >= 0 or not inSameChain(resId1, resId2, oa.chain_starts, oa.chain_ends): + res_table[0][i][j] = 1 + else: + res_table[0][i][j] = 0 + + + if z_dependent or inMembrane: + mem_gamma_direct, mem_gamma_mediated = read_gamma(os.path.join(parametersLocation, membraneGammaName)) + m = 1 # membrane environment + count = 0 + for i in range(20): + for j in range(i, 20): + gamma_ijm[m][i][j] = mem_gamma_direct[count][0]*k_relative_mem + gamma_ijm[m][j][i] = mem_gamma_direct[count][0]*k_relative_mem + count += 1 + count = 0 + for i in range(20): + for j in range(i, 20): + water_gamma_ijm[m][i][j] = mem_gamma_mediated[count][1]*k_relative_mem + water_gamma_ijm[m][j][i] = mem_gamma_mediated[count][1]*k_relative_mem + count += 1 + count = 0 + for i in range(20): + for j in range(i, 20): + protein_gamma_ijm[m][i][j] = mem_gamma_mediated[count][0]*k_relative_mem + protein_gamma_ijm[m][j][i] = mem_gamma_mediated[count][0]*k_relative_mem + count += 1 + for i in range(oa.nres): + for j in range(oa.nres): + resId1 = i + resId2 = j + if abs(resId1-resId2)-min_sequence_separation_mem >= 0 or not inSameChain(resId1, resId2, oa.chain_starts, oa.chain_ends): + res_table[m][i][j] = 1 + else: + res_table[m][i][j] = 0 + + contact.addTabulatedFunction("gamma_ijm", Discrete3DFunction(nwell, 20, 20, gamma_ijm.T.flatten())) + contact.addTabulatedFunction("water_gamma_ijm", Discrete3DFunction(nwell, 20, 20, water_gamma_ijm.T.flatten())) + contact.addTabulatedFunction("protein_gamma_ijm", Discrete3DFunction(nwell, 20, 20, protein_gamma_ijm.T.flatten())) + contact.addTabulatedFunction("burial_gamma_ij", Discrete2DFunction(20, 3, burial_gamma.T.flatten())) + contact.addTabulatedFunction("res_table", Discrete3DFunction(nwell, oa.nres, oa.nres, res_table.T.flatten())) + contact.addTabulatedFunction("inSameChain",Discrete2DFunction(oa.nres, oa.nres, np.array([[int(inSameChain(i,j,oa.chain_starts,oa.chain_ends)) for j in range(oa.nres)] for i in range(oa.nres)]).T.flatten())) + if direct_mask_ij is not None: + contact.addTabulatedFunction("direct_ij", Discrete2DFunction(oa.nres,oa.nres,direct_mask_ij.T.flatten())) + if protein_mask_ij is not None: + contact.addTabulatedFunction("protein_ij", Discrete2DFunction(oa.nres,oa.nres,protein_mask_ij.T.flatten())) + if water_mask_ij is not None: + contact.addTabulatedFunction("water_ij", Discrete2DFunction(oa.nres,oa.nres,water_mask_ij.T.flatten())) + contact.addTabulatedFunction("helicalHB_gamma_i", Discrete1DFunction(helical_gamma_i)) + + contact.addPerParticleParameter("resName") + contact.addPerParticleParameter("resId") + contact.addPerParticleParameter("isCb") + contact.addPerParticleParameter("isO") + contact.addPerParticleParameter("isN") + contact.addPerParticleParameter("isH") + + contact.addComputedValue("rho", f"isCb1*isCb2*step(abs(resId1-resId2)-2)*0.25*(1+tanh({eta}*(r-{r_min})))*(1+tanh({eta}*({r_max}-r)))", CustomGBForce.ParticlePair) + #contact.addComputedValue("rho_test",f"isCb1*isCb2*step(abs(resId1-resId2)-2)", CustomGBForce.ParticlePair) + + # if z_dependent: + # contact.addComputedValue("isInMembrane", f"step({z_m}-abs(z))", CustomGBForce.SingleParticle) + # else: + # contact.addComputedValue("isInMembrane", "0", CustomGBForce.SingleParticle) + + + # mingchen/weihua defined the sharpness of the switching function differently for the helical hbonds for some reason, + # so it technically requires us to compute a new rho + contact.addComputedValue("rho_forHB", f"isCb1*isCb2*step(abs(resId1-resId2)-2)*0.25*(1+tanh({helix_eta}*(r-{r_min})))*(1+tanh({helix_eta}*({r_max}-r)))", CustomGBForce.ParticlePair) + # for the hbonds, assign the Oi to Nip4 distance to particle Oi + # and also assign the Oi to Hip4 distance to particle Oi + # and also assign the sigma of i and ip4 to particle Oi + # and also assign a bool of whether i and ip4 are in the same chain, multiplied by the sum of propensities, to particle Oi + contact.addComputedValue("r_Oi_Nip4_forHB", "isO1*isN2*delta((resId2-resId1)-4)*r", CustomGBForce.ParticlePair) + contact.addComputedValue("r_Oi_Hip4_forHB", "isO1*isH2*delta((resId2-resId1)-4)*r", CustomGBForce.ParticlePair) + contact.addComputedValue("other_rho_forHB", "isO1*isCb2*delta((resId2-resId1)-4)*rho_forHB2", CustomGBForce.ParticlePair) + contact.addComputedValue("sigma_forHB", f"isO*0.25*(1-tanh({helix_eta_sigma}*(rho_forHB-{helix_rho_0})))*(1-tanh({helix_eta_sigma}*(other_rho_forHB-{rho_0})))", CustomGBForce.SingleParticle) + contact.addComputedValue("weight_forHB", f"isO1*isN2*delta((resId2-resId1)-4)*inSameChain(resId1,resId2)*\ + (helicalHB_gamma_i(resName1)+helicalHB_gamma_i(resName2))", CustomGBForce.ParticlePair) + # calculate the helical hbond energy between residues i and i+4 using the values assigned to particle Oi + k_helical *= oa.k_awsem + sigma_NO = 0.068 + sigma_HO = 0.076 + r_ON = 0.298 # mingchen/weihua used 2.9862, at least for the helical hbond sigma + r_OH = 0.206 # mingchen/weihua used 2.1558, at least for the helical hbond sigma + theta_ij = f"exp(-(r_Oi_Nip4_forHB-{r_ON})^2/(2*{sigma_NO}^2)-(r_Oi_Hip4_forHB-{r_OH})^2/(2*{sigma_HO}^2))" + helical_hbond_energy_string = f"-{k_helical}*((1-sigma)*2+sigma*(-1))*weight_forHB*{theta_ij}" + contact.addEnergyTerm(helical_hbond_energy_string, CustomGBForce.SingleParticle) + + # contact.addComputedValue("isInMembrane", "1", CustomGBForce.SingleParticle) + # replace cb with ca for GLY + cb_fixed = [x if x > 0 else y for x,y in zip(oa.cb,oa.ca)] + none_cb_fixed = [i for i in range(oa.natoms) if i not in cb_fixed] + assert len(cb_fixed) == oa.nres, f"Number of atoms in cb_fixed (non-GLY CB and GLY CA atoms), {len(cb_fixed)}, does not match number of residues {oa.nres}." + # print(oa.natoms, len(oa.resi), oa.resi, seq) + for i in range(oa.natoms): + contact.addParticle([gamma_se_map_1_letter[seq[oa.resi[i]]], oa.resi[i], int(i in cb_fixed), int(i in oa.o), int(i in oa.n), int(i in oa.h)]) + + # SET UP PAIRWISE FORCE + def base_contact_energy(inMembrane): + # to avoid nested if statements, DIRECT_MASK, WATER_MASK, and PROTEIN_MASK + # will be replaced later + direct_base = f"DIRECT_MASK gamma_ijm({inMembrane}, resName1, resName2)" + water_base = f"WATER_MASK sigma_water*water_gamma_ijm({inMembrane}, resName1, resName2)" + protein_base = f"PROTEIN_MASK sigma_protein*protein_gamma_ijm({inMembrane}, resName1, resName2)" + return f"res_table({inMembrane},resId1,resId2)*({direct_base}*theta+thetaII*({water_base}+{protein_base}))" + + #Modify the contact force to include z-dependent membrane interaction + if z_dependent: + contact.addComputedValue("alphaMembrane", + f"0.5*tanh({eta_switching}*((z-{membrane_center})+{z_m}))+0.5*tanh({eta_switching}*({z_m}-(z-{membrane_center})))", + CustomGBForce.SingleParticle) + base_energy_string = f"(1-alphaMembrane1*alphaMembrane2)*{base_contact_energy(0)}\ + +(alphaMembrane1*alphaMembrane2)*{base_contact_energy(1)};" + else: + base_energy_string = f"{base_contact_energy(inMembrane)};" + + # Modify the base energy string to include weights for direct, water, and protein interactions + if direct_mask_ij is not None: + base_energy_string = base_energy_string.replace("DIRECT_MASK ", "direct_ij(resId1, resId2)*") + else: + base_energy_string = base_energy_string.replace("DIRECT_MASK ", "") + if protein_mask_ij is not None: + base_energy_string = base_energy_string.replace("PROTEIN_MASK ", "protein_ij(resId1, resId2)*") + else: + base_energy_string = base_energy_string.replace("PROTEIN_MASK", "") + if water_mask_ij is not None: + base_energy_string = base_energy_string.replace("WATER_MASK", "water_ij(resId1, resId2)*") + else: + base_energy_string = base_energy_string.replace("WATER_MASK", "") + + #Add other coefficients and definitions to the energy string + coefficients = f"-isCb1*isCb2*{k_contact}*" + definitions = f"sigma_protein=1-sigma_water;\ + theta=0.25*(1+tanh({eta}*(r-{r_min})))*(1+tanh({eta}*({r_max}-r)));\ + thetaII=0.25*(1+tanh({eta}*(r-{r_minII})))*(1+tanh({eta}*({r_maxII}-r)));\ + sigma_water=0.25*(1-tanh({eta_sigma}*(rho1-{rho_0})))*(1-tanh({eta_sigma}*(rho2-{rho_0})))" + + energy_string = f"{coefficients}{base_energy_string}{definitions}" + #print("Contact energy string: ", energy_string) + + # use energy expression to the ParticlePair interaction + contact.addEnergyTerm(energy_string, CustomGBForce.ParticlePair) + + # SET UP THE BURIAL FORCE + if burialPartOn: + for i in range(3): + contact.addGlobalParameter(f"rho_min_{i}", burial_ro_min[i]) + contact.addGlobalParameter(f"rho_max_{i}", burial_ro_max[i]) + for i in range(3): + contact.addEnergyTerm(f"-0.5*isCb*{k_burial}*burial_gamma_ij(resName, {i})*\ + (tanh({burial_kappa}*(rho-rho_min_{i}))+\ + tanh({burial_kappa}*(rho_max_{i}-rho)))", CustomGBForce.SingleParticle) + + + print("Number of atom: ", oa.natoms, "Number of residue: ", len(cb_fixed)) + # print(len(none_cb_fixed), len(cb_fixed)) + + # withExclusion won't affect the result. But may speed up the calculation with CPU but slows down for GPU. + if withExclusion: + for e1 in none_cb_fixed: + for e2 in none_cb_fixed: + if e1 > e2: + continue + contact.addExclusion(e1, e2) + for e1 in none_cb_fixed: + for e2 in cb_fixed: + contact.addExclusion(e1, e2) + + # contact.setCutoffDistance(1.1) + if oa.periodic_box: + contact.setNonbondedMethod(contact.CutoffPeriodic) + print('\ncontact_term is periodic') + else: + contact.setNonbondedMethod(contact.CutoffNonPeriodic) + print("Contact cutoff ", contact.getCutoffDistance()) + print("NonbondedMethod: ", contact.getNonbondedMethod()) + contact.setForceGroup(forceGroup) + return contact + +def contact_term( + oa, k_contact=4.184, k_burial = None, z_dependent=False, z_m=1.5, inMembrane=False, membrane_center=0*angstrom, k_relative_mem=1.0, parametersLocation=None, burialPartOn=True, withExclusion=False, forceGroup=22, + gammaName="gamma.dat", burialGammaName="burial_gamma.dat", membraneGammaName="membrane_gamma.dat", r_min=0.45,min_sequence_separation=10,min_sequence_separation_mem=10, + direct_mask_ij=None, water_mask_ij=None, protein_mask_ij=None): # set up masks to reweight contacts if direct_mask_ij is not None and direct_mask_ij.shape != (oa.nres, oa.nres): raise ValueError(f"direct_mask_ij should be of shape {(oa.nres, oa.nres)}, but got {direct_mask_ij.shape}") diff --git a/openawsem/functionTerms/hydrogenBondTerms.py b/openawsem/functionTerms/hydrogenBondTerms.py index ca785c4a..0bf8b763 100644 --- a/openawsem/functionTerms/hydrogenBondTerms.py +++ b/openawsem/functionTerms/hydrogenBondTerms.py @@ -441,7 +441,10 @@ def pap_term_1(oa, k=0.5*kilocalories_per_mole, dis_i_to_i4=1.2, forceGroup=28, https://github.com/adavtyan/awsemmd/tree/cea754f1208fde6332d4d0f1cae3212bf7e8afbb, within a tolerance of 0.01 kcal/mol on all tested systems and computational Platforms. It should be noted that not all LAMMPS AWSEM-MD versions are identical. - However, the LAMMPS AWSEM-MD potential is implemented as a single term that should be accessed using pap_term_old. + I believe using pap_nu_on=False with version='efficiency_optimized' is equivalent to but maybe more efficient than + using version='lammps_awsemmd' (pap_nu_on is irrelevant in this case). I'll check this soon. + + The rigorously tested LAMMPS AWSEM-MD potential is implemented as a single term that should be accessed using pap_term_old. The OpenAWSEM paper: Lu, W.; Bueno, C.; Schafer, N. P.; Moller, J.; Jin, S.; Chen, X.; Chen, M.; Gu, X.; @@ -491,7 +494,10 @@ def pap_term_2(oa, k=0.5*kilocalories_per_mole, dis_i_to_i4=1.2, forceGroup=28, https://github.com/adavtyan/awsemmd/tree/cea754f1208fde6332d4d0f1cae3212bf7e8afbb, within a tolerance of 0.01 kcal/mol on all tested systems and computational Platforms. It should be noted that not all LAMMPS AWSEM-MD versions are identical. - However, the LAMMPS AWSEM-MD potential is implemented as a single term that should be accessed using pap_term_old. + I believe using pap_nu_on=False with version='efficiency_optimized' is equivalent to but maybe more efficient than + using version='lammps_awsemmd' (pap_nu_on is irrelevant in this case). I'll check this soon. + + The rigorously tested LAMMPS AWSEM-MD potential is implemented as a single term that should be accessed using pap_term_old. The OpenAWSEM paper: Lu, W.; Bueno, C.; Schafer, N. P.; Moller, J.; Jin, S.; Chen, X.; Chen, M.; Gu, X.; @@ -536,41 +542,274 @@ def pap_term_old(oa, k_pap=4.184, forceGroup=26, ssweight_file="ssweight", enabl def helical_term(oa, k_helical=4.184, inMembrane=False, forceGroup=29): """ - Note that this term is not exactly the same as the LAMMPS AWSEM-MD helical term. - I think the only difference is the treatment of proline at the i+4 position. - Changing this to make it exactly like lammps would be difficult and possibly cost us some efficiency. + We can think of this as the "default" or "efficiency-optimized" helical term + written by Lu et al. around 2020. + + This term is not exactly the same as the LAMMPS AWSEM-MD helical term. + The major difference is that this term doesn't consider the sigma_helix (analogous to + sigma_wat but possibly with different parameters) of the pair of residues + involved in the hydrogen bonding interaction (see density_dependent_helical_term + for explanation). + + Another difference is that, since we don't have a virtual particle for the proline + backbone H (which doesn't exist in reality), it can't act as a donor. + Here, we simply turn off the potential in the case that proline is in the donor position. + + In LAMMPS, proline in the donor (i+4) position is allowed to participate in an hbond interaction, + but the default proline weight makes the interaction strongly unfavorable. + Having a hydrogen bond with proline in the acceptor (i) position can then be made + more favorable by the pro_accepter_flag argument and passing a more favorable + weight than the normal unfavorable weight. For example: + [Helix] + 0.5 + 2.0 -1.0 + 7.0 7.0 + 3.0 + 4 + 15.0 + 4.5 6.5 + 0.77 0.68 0.07 0.15 0.23 0.33 0.27 0.0 0.06 0.23 0.62 0.65 0.50 0.41 -3.0 0.35 0.11 0.45 0.17 0.14 + 0 -3.0 <-- 0 is pro_accepter_flag, so proline will get the default weight of -3.0 for both i and i+4 positions + and even if we had set it to 1, the second number, -3.0, is the same as the default, so it + wouldn't have mattered. But we could change 0 -> 1 and -3.0 -> something else + 0.76 0.68 + 2.1558 2.9862 """ - # without density dependency. - # without z dependency for now. + # some useful parameters k_helical *= oa.k_awsem sigma_NO = 0.068 sigma_HO = 0.076 - r_ON = 0.298 - r_OH = 0.206 + r_ON = 0.298 # mingchen/weihua used a slightly different number (0.21558 nm) + r_OH = 0.206 # mingchen/weihua used a slightly different number (0.29862 nm) + # theta_ij checks whether our O_i, N_i+4, and H_i+4 are in an H-bond geometry theta_ij = f"exp(-(r_Oi_Nip4-{r_ON})^2/(2*{sigma_NO}^2)-(r_Oi_Hip4-{r_OH})^2/(2*{sigma_HO}^2))" + + #declare 3-body Force helical = CustomCompoundBondForce(3, f"-{k_helical}*(fa_i+fa_ip4)*{theta_ij};\ r_Oi_Nip4=distance(p1,p2);r_Oi_Hip4=distance(p1,p3);") + + # add per-amino-acid helical propensities helical.addPerBondParameter("fa_i") helical.addPerBondParameter("fa_ip4") + + # add a Bond to the Force for each (i, i+4) pair for i in range(oa.nres): - # if not isChainEnd(i, oa.chain_ends, n=4) and oa.res_type[i+4] == "IPR": - # print(oa.o[i], oa.n[i+4], oa.h[i+4]) if not isChainEnd(i, oa.chain_ends, n=4) and oa.res_type[i+4] != "IPR": fa_i = get_helical_f(oa.seq[i], inMembrane=inMembrane) fa_ip4 = get_helical_f(oa.seq[i+4], inMembrane=inMembrane) helical.addBond([oa.o[i], oa.n[i+4], oa.h[i+4]], [fa_i, fa_ip4]) + # finalize setup and return Force helical.setForceGroup(forceGroup) return helical +def density_dependent_helical_term(oa, k_helical=4.184, inMembrane=False, forceGroup=29): + # we avoid get_helical_f here so that we can reproduce old work + helical_gamma_i=[0.77,0.68,0.07,0.15,0.23,0.33,0.27,0.0,0.06,0.23,0.62,0.65,0.50,0.41,-3.0,0.35,0.11,0.45,0.17,0.14] + arnd = 'ARNDCQEGHILKMFPSTWYV' + """ + WARNING: THIS TERM IS EXPECTED TO BE VERY SLOW AND/OR RAM-INTENSIVE + FOR ALL BUT THE SMALLEST SYSTEMS. + SEE density_dependent_helical_term_approximate FOR AN ALTERNATIVE. + + This is the exact density-dependent helical term calculated by lammps commit + https://github.com/adavtyan/awsemmd/tree/cea754f1208fde6332d4d0f1cae3212bf7e8afbb + using the following vitural site and helical parameters: + [ABC] + 0.4831806 0.703282 -0.1864262 + 0.4436538 0.2352006 0.3211455 + 0.841 0.89296 -0.73389 + [Helix] + 0.5 + 2.0 -1.0 + 7.0 7.0 + 3.0 + 4 + 15.0 + 4.5 6.5 + 0.77 0.68 0.07 0.15 0.23 0.33 0.27 0.0 0.06 0.23 0.62 0.65 0.50 0.41 -3.0 0.35 0.11 0.45 0.17 0.14 + 0 -3.0 + 0.76 0.68 + 2.1558 2.9862 + + This term is similar to helical_term, except it includes the sigma_helix factor in the energy expression + and creates a hydrogen pseudoatom on the proline N so it can be treated like the other residues. + + sigma_helix is analogous to sigma_water but its default parameters are different. + Both sigma_helix and sigma_water assign a pair of residues as either exposed or buried + based on the rho values of the two residues in the pair. The "sigma_helix factor" + linearly interpolates between +2 and -1 as sigma_helix goes from 0 (buried residues) + to 1 (exposed residues), reflecting that helices are somewhat less stable in + solvent-exposed environments than in buried environments. + + The modern density-dependent helical potential was introduced in + 2010 (doi.org/10.1016/j.ymeth.2010.05.006). As noted in this paper, the roots of + the helical potential go back to 1999 (doi.org/10.1063/1.479101). + + Strangely, the helical conformation actually becomes favorable for proline in a + solvent-exposed environment. This is because the sum of the default proline + helical propensity (-3.0) with any other residue's helical propensity (>= 0) + is a fairly big negative number which, when multiplied by the default weight + for the water environment of -1.0, and then by the coefficient of -k_helical, + gives a negative (favorable) potential. It would probably make more sense to + just exclude pairs (i,i+4) with PRO at i+4 from the potential. + """ + if inMembrane: + raise NotImplementedError("inMembrane option=True not supported for density_dependent_helical_term") + + # some useful parameters + k_helical *= oa.k_awsem + sigma_NO = 0.068 + sigma_HO = 0.076 + r_ON = 0.29862#0.298 # mingchen/weihua used 2.9862, at least for the helical hbond sigma + r_OH = 0.21558#0.206 # mingchen/weihua used 2.1558, at least for the helical hbond sigma + # parameters for the sigma involved in the helical hbonds + helix_eta = 7 # CAREFUL: THIS NUMBER HAS UNITS OF 1/ANGSTROM, SO WE MULTIPLY THE DISTANCES (IN nm) BY 10 (SEE BELOW) + helix_eta_sigma = 7.0 + helix_rho_0 = 3.0 + + # interpolates between favorable and unfavorable weights for burial and exposed pairs, respectively + sigma_helix_term = '(2-3*sigma_helix)' # equal to (helix_gamma_p*(1-sigma_helix)+helix_gamma_w*sigma_helix), where helix_gamma_p=2, helix_gamma_w=-1 + + # characterizes the compatibility of O_i, N_i+4, and H_i+4 with hydrogen bonding + theta_helix = f"exp(-(distance(p1,p2)-{r_ON})^2/(2*{sigma_NO}^2)-(pointdistance(x1,y1,z1,xh,yh,zh)-{r_OH})^2/(2*{sigma_HO}^2))" + + # Create rho expressions to help us select the needed rho value for each residue. + # + # This expression is the sum of the rho value of each residue multiplied by + # a delta function that depends on the PerBondParameter i. Each Bond sets + # i to the 0-indexed position of the acceptor or donor residue + # so that the density of that residue can be isolated. + rho_i = "(0" + for i in range(oa.nres): + rho_i += f"+delta({i}-i)*(0" # multiply delta function by density of residue i + for j in range(oa.nres): # create string representing density of residue i + if abs(j-i) >= 2: # get contribution of residue j to the rho of residue i + r_ij = f'10*distance(p{i+6},p{j+6})' + rho_i += f"+0.25*(1+tanh({helix_eta}*({r_ij}-4.5)))*(1+tanh({helix_eta}*(6.5-{r_ij})))" + else: + continue # we would have violated min seq sep rho of 2 if we included this residue in the rho calculation + rho_i += ')' + rho_i += ')' + rho_ip4 = "(0" + for i in range(4,oa.nres): + rho_ip4 += f"+delta({i-4}-i)*(0" + for j in range(oa.nres): + if abs(j-i) >= 2: + r_ip4j = f'10*distance(p{i+6},p{j+6})' + rho_ip4 += f"+0.25*(1+tanh({helix_eta}*({r_ip4j}-4.5)))*(1+tanh({helix_eta}*(6.5-{r_ip4j})))" + rho_ip4 += ')' + rho_ip4 += ')' + + # get hydrogen pseudoatom coordinates (this allows us to treat IPR (proline) like the other residues) + definitions = f';xh=0.841*x4+0.89296*x5-0.73389*x3;yh=0.841*y4+0.89296*y5-0.73389*y3;zh=0.841*z4+0.89296*z5-0.73389*z3\ + ;sigma_helix=0.25*(1-tanh({helix_eta_sigma}*({rho_i}-{helix_rho_0})))*(1-tanh({helix_eta_sigma}*({rho_ip4}-{helix_rho_0})))' + energy_string = f'-{k_helical}*{sigma_helix_term}*(helical_propensities(i)+helical_propensities(i+4))*{theta_helix}{definitions}' + + # set up Force + HB = CustomCompoundBondForce(6+oa.nres-1, energy_string) # see below for how we calculate the number of atoms needed + HB.addPerBondParameter("i") # note that we don't use get_helical_f here because it has a different proline parameter + HB.addTabulatedFunction('helical_propensities', Discrete1DFunction([helical_gamma_i[arnd.index(one_letter_code)] for one_letter_code in oa.seq])) + + # get particle indices and set up each Bond + # index 1: Oi (needed to calculate geometric compatibility with H bond) + # index 2: Nip4 (needed to calculate geometric compatibility with H bond) + # index 3: Oip3 (needed to calculate position of hip4, used to calculate geometric compatibility with H bond) + # index 4: CAip3 (needed to calculate position of hip4) + # index 5: CAip4 (needed to calculate position of hip4) + # indices 6 to 6+N-1: CB atoms, from residue 1 to N (needed to calculate rho); + for i in range(oa.nres-4): + if inSameChain(i, i+4, oa.chain_starts, oa.chain_ends): + # we should add a bond + particles = [oa.o[i], oa.n[i+4], oa.o[i+3], oa.ca[i+3], oa.ca[i+4]] + cb_fixed = [x if x > 0 else y for x,y in zip(oa.cb,oa.ca)] + particles += cb_fixed + assert len(particles) == oa.nres+5, particles + HB.addBond(particles, [i]) # perbondparameter "i" indicates the 0-indexed residue index of the acceptor + HB.setForceGroup(forceGroup) + return HB + +def density_dependent_helical_term_approximate(oa, k_helical=4.184, inMembrane=False, forceGroup=29): + # we avoid get_helical_f here so that we can reproduce old work -3.0 + helical_gamma_i=[0.77,0.68,0.07,0.15,0.23,0.33,0.27,0.0,0.06,0.23,0.62,0.65,0.50,0.41,0.0,0.35,0.11,0.45,0.17,0.14] + arnd = 'ARNDCQEGHILKMFPSTWYV' + # just do this for now until we decide how to implement membrane parameters + if inMembrane: + raise NotImplementedError("still figuring out how density-dependent helical term should mix with membrane gammas") + """ + Efficient approximation to density_dependent_helical_term with density dependence. + The approximation lies in the use of combined attractive and repulsive PAIRWISE interactions + to give an effectively directional hydrogen bond. + """ + # the general implementation strategy here is to use a CustomCompoundBondForce + # to get rho just like we do for the contact term, then add pairwise energy terms + # to the Force to implement the attractive and repulsive interactions ONLY + # between residues i and i+4. Since pairs (i,i+4) are excluded from the Beta + # and P-AP hydrogen bonding terms, there shouldn't be any side effects of + # changing the form of the interaction; we just want to get as close as + # reasonably possible to the lammps version. + + # some useful parameters + k_helical *= oa.k_awsem + sigma_NO = 0.068 + sigma_HO = 0.076 + r_ON = 0.29862#0.298 # mingchen/weihua used 2.9862, at least for the helical hbond sigma + r_OH = 0.21558#0.206 # mingchen/weihua used 2.1558, at least for the helical hbond sigma + # parameters for the sigma involved in the helical hbonds + helix_eta = 7 # CAREFUL: THIS NUMBER HAS UNITS OF 1/ANGSTROM, SO WE MULTIPLY THE DISTANCES (IN nm) BY 10 (SEE BELOW) + helix_eta_sigma = 7.0 + helix_rho_0 = 3.0 + + # set up Force + HB = CustomGBForce() + HB.addPerParticleParameter("resId") + HB.addPerParticleParameter("isCb") + HB.addPerParticleParameter("isN") + HB.addPerParticleParameter("isO") + HB.addPerParticleParameter("isCa") + HB.addPerParticleParameter("isCp") # C prime (backbone carbonyl carbon) + HB.addTabulatedFunction('helical_propensities', Discrete1DFunction([helical_gamma_i[arnd.index(one_letter_code)] for one_letter_code in oa.seq])) + # HB.addTabulatedFunction('helical_propensities', Discrete1DFunction([get_helical_f(oa.seq[i], inMembrane=inMembrane) for one_letter_code in oa.seq])) + # should consider contributes for residue with sequence separation of less that 2 (meaning 1) if + # the two residues are in different chains + HB.addComputedValue("rho", f"isCb1*isCb2*step(abs(resId1-resId2)-2)*0.25*(1+tanh({helix_eta}*(10*r-4.5)))*(1+tanh({helix_eta}*(6.5-10*r)))", CustomGBForce.ParticlePair) + + # add particles to Force + # replace cb with ca for GLY + cb_fixed = [x if x > 0 else y for x,y in zip(oa.cb,oa.ca)] + none_cb_fixed = [i for i in range(oa.natoms) if i not in cb_fixed] + assert len(cb_fixed) == oa.nres, f"Number of atoms in cb_fixed (non-GLY CB and GLY CA atoms), {len(cb_fixed)}, does not match number of residues {oa.nres}." + for i in range(oa.natoms): + HB.addParticle([oa.resi[i], int(i in cb_fixed), int(i in oa.n), int(i in oa.o), int(i in oa.ca), int(i in oa.c)]) + + # define energy + #definitions = f';sigma_helix_term=2\ + definitions = f';sigma_helix_term=(2-3*sigma_helix)\ + ;sigma_helix=0.25*(1-tanh({helix_eta_sigma}*(rho1-{helix_rho_0})))*(1-tanh({helix_eta_sigma}*(rho2-{helix_rho_0})))\ + ;propensity=(helical_propensities(resId1)+helical_propensities(resId2))\ + ;LJ=(-isO1*isN2*tanh(0.03*((2/(10*r-3.43))^2))+(isCp1*isCp2+isCp1*isCa2+isCa1*isN2+isN1*isN2)*tanh(0.03*((2/(10*r-2))^2)))' + #;LJ=(-isO1*isN2*tanh(0.03*((2/(10*r-3.43))^2)))' + #;LJ=(-isO1*isN2+isCp1*isCp2+isCp1*isCa2)*tanh(0.03*((2/(10*r-3.43))^2))' + #;LJ=isO1*isN2*(5*((2.0/(10*r-1.43))^(12))-6*((2.0/(10*r-1.43))^(10)))' # converting r from nm to Angstrom to match units of constants + # no leading negative sign in energy string because LJ term is sort of like a negative helix theta + energy_string = f"{k_helical}*delta((resId2-resId1)-4)*sigma_helix_term*propensity*LJ{definitions}" + HB.addEnergyTerm(energy_string, CustomGBForce.ParticlePair) + + # finalize and return Force + # cutoff shouldn't matter because i and i+4 should always be close in space + if oa.periodic_box: + HB.setNonbondedMethod(HB.CutoffPeriodic) + else: + HB.setNonbondedMethod(HB.CutoffNonPeriodic) + HB.setForceGroup(forceGroup) + return HB + def sequence_independent_helical_term(oa, k_helical=4.184, inMembrane=False, forceGroup=29): """ Experimental sequence-independent helical term for folding designed sequences """ - - # without density dependency. - # without z dependency for now. + # see helical_term for helpful comments on parameters and code in this function k_helical *= oa.k_awsem sigma_NO = 0.068 sigma_HO = 0.076 @@ -742,7 +981,7 @@ def _beta_lammps_awsemmd(oa, term_number, ssweight_file, forceGroup, k_beta, bet # so there's no need to add a bond if |i-j|=3 continue # if sequence separation is less than 18, i and j are in the same chain, and both are not designated as beta in ssweight, - # then we alway set the energy to 0, so we can just exclude the Bond from the Force + # then we always set the energy to 0, so we can just exclude the Bond from the Force elif abs(i-j) < 18 and inSameChain(i, j, oa.chain_starts, oa.chain_ends) and (rama_biases[i][1]==0 or rama_biases[j][1]==0): continue # the lammps code excludes certain pairs of residues from Beta2 but not the others @@ -979,10 +1218,10 @@ def _pap_lammps_awsemmd(oa, ssweight_file, forceGroup, k_pap, enable_antiparalle # Not a valid i continue for j in range(nres): - # check if we may be able to add an antiparallel hydrogen bond delta = j-i intrachain = inSameChain(i,j,oa.chain_starts,oa.chain_ends) if enable_antiparallel: + # check if we may be able to add an antiparallel hydrogen bond if not inSameChain(j,j-4,oa.chain_starts,oa.chain_ends): K = 0 # Not a valid j elif intrachain and delta < 13: @@ -995,9 +1234,10 @@ def _pap_lammps_awsemmd(oa, ssweight_file, forceGroup, k_pap, enable_antiparalle K *= k_beta_pred_p_ap else: raise AssertionError("unexpected else block") - if K: + if K: # add the Bond unless its energy would always be 0 pap.addBond([ca[i],ca[j],ca[i+4],ca[j-4]], [K]) if enable_parallel: + # check if we may be able to add a parallel hydrogen bond if not inSameChain(j,j+4,oa.chain_starts,oa.chain_ends): K=0 #Not a valid j elif intrachain and delta < 9: @@ -1006,9 +1246,9 @@ def _pap_lammps_awsemmd(oa, ssweight_file, forceGroup, k_pap, enable_antiparalle K = gamma_p*k_beta_pred_p_ap else: K = gamma_p - if K: + if K: # add the Bond unless its energy would always be 0 pap.addBond([ca[i],ca[j],ca[i+4],ca[j+4]], [K]) - + # finalize and return Force pap.setForceGroup(forceGroup) return pap diff --git a/openawsem/functionTerms/templateTerms.py b/openawsem/functionTerms/templateTerms.py index 0cfc4f19..ea8ceb28 100644 --- a/openawsem/functionTerms/templateTerms.py +++ b/openawsem/functionTerms/templateTerms.py @@ -67,6 +67,31 @@ def tbm_q_term(oa, k_tbm_q, rnative_dat="rnative.dat", tbm_q_min_seq_sep=3, tbm_ return tbm_q +def interface_q_term(oa, pairs, rnatives, sigma, target_q, k, forceGroup=26): + """ + oa: same as always + pairs: list of lists, where each sublist contains two atom indices, one on either side of the interface + rnatives: list of target distances of the same length as pairs, in nm + sigma: sigma of the gaussian function, in nm; + target_q: q value having minimum penalty (bias function equal to 0) + k: stiffness of q restraint, in kJ/mol (bias = (1/2)k*(q-target_q)^2) + """ + print("Interface Q term ON") + assert len(pairs) == len(rnatives) + # set up collective variable, q + q = CustomBondForce(f"(1/{len(rnatives)})*gamma_ij*exp(-(r-r_ijN)^2/(2*sigma_ij^2))") + q.addPerBondParameter("gamma_ij") + q.addPerBondParameter("r_ijN") + q.addPerBondParameter("sigma_ij") + for pair, rnative in zip(pairs, rnatives): + #print([pair[0], pair[1], [1.0, rnative, sigma]]) + q.addBond(pair[0], pair[1], [1.0, rnative, sigma]) + # set up Force + q_force = CustomCVForce(f"{k}*(q-{target_q})^2") + q_force.addCollectiveVariable("q", q) + q_force.setForceGroup(forceGroup) + return q_force + def fragment_memory_term(oa, k_fm=0.04184, frag_file_list_file="./frag.mem", npy_frag_table="./frag_table.npy", min_seq_sep=3, max_seq_sep=9, fm_well_width=0.1, UseSavedFragTable=True, caOnly=False, forceGroup=23, diff --git a/openawsem/openAWSEM.py b/openawsem/openAWSEM.py index b359fe51..85b60490 100644 --- a/openawsem/openAWSEM.py +++ b/openawsem/openAWSEM.py @@ -151,6 +151,8 @@ class BaseError(Exception): class Protein(object): def __init__(self, atoms, sequence, k_awsem=1): self.atoms = atoms + self.periodic_box = None + self.fixed_residue_indices = [] #Include real residue name in atoms atoms = self.atoms.copy() diff --git a/openawsem/topology/awsem.xml b/openawsem/topology/awsem.xml index 21881633..a1004f91 100644 --- a/openawsem/topology/awsem.xml +++ b/openawsem/topology/awsem.xml @@ -3,10 +3,10 @@ - + - - + + @@ -79,4 +79,4 @@ - \ No newline at end of file + diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/2mlt_1to5-crystal_structure.fasta b/tests/data/test_implementation_of_lammps_hbond_energies/2mlt_1to5-crystal_structure.fasta new file mode 100644 index 00000000..f778ea1f --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/2mlt_1to5-crystal_structure.fasta @@ -0,0 +1,2 @@ +>CRYSTAL_STRUCTURE:A +GIGAV diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/2mlt_1to5-crystal_structure.pdb b/tests/data/test_implementation_of_lammps_hbond_energies/2mlt_1to5-crystal_structure.pdb new file mode 100644 index 00000000..81a423a1 --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/2mlt_1to5-crystal_structure.pdb @@ -0,0 +1,66 @@ +REMARK 1 CREATED WITH OPENMM 8.1.1, 2025-12-22 +CRYST1 60.832 38.293 42.211 90.00 90.00 90.00 P 1 1 +ATOM 1 N GLY A 1 42.375 -12.180 24.780 1.00 0.00 N +ATOM 2 H GLY A 1 41.203 -12.267 24.564 1.00 0.00 H +ATOM 3 H2 GLY A 1 42.656 -13.342 24.695 1.00 0.00 H +ATOM 4 H3 GLY A 1 42.346 -11.870 25.939 1.00 0.00 H +ATOM 5 CA GLY A 1 43.603 -11.488 24.325 1.00 0.00 C +ATOM 6 HA2 GLY A 1 44.282 -11.310 25.295 1.00 0.00 H +ATOM 7 HA3 GLY A 1 44.281 -12.169 23.614 1.00 0.00 H +ATOM 8 C GLY A 1 43.288 -10.171 23.615 1.00 0.00 C +ATOM 9 O GLY A 1 42.111 -9.896 23.277 1.00 0.00 O +ATOM 10 N ILE A 2 44.323 -9.391 23.299 1.00 0.00 N +ATOM 11 H ILE A 2 45.382 -9.730 23.721 1.00 0.00 H +ATOM 12 CA ILE A 2 44.200 -8.183 22.475 1.00 0.00 C +ATOM 13 HA ILE A 2 43.357 -7.499 22.957 1.00 0.00 H +ATOM 14 C ILE A 2 43.750 -8.629 21.119 1.00 0.00 C +ATOM 15 O ILE A 2 43.068 -7.904 20.409 1.00 0.00 O +ATOM 16 CB ILE A 2 45.525 -7.320 22.425 1.00 0.00 C +ATOM 17 HB ILE A 2 46.495 -7.948 22.119 1.00 0.00 H +ATOM 18 CG1 ILE A 2 45.924 -6.837 23.820 1.00 0.00 C +ATOM 19 HG12 ILE A 2 46.767 -5.985 23.815 1.00 0.00 H +ATOM 20 HG13 ILE A 2 46.566 -7.648 24.425 1.00 0.00 H +ATOM 21 CG2 ILE A 2 45.555 -6.173 21.386 1.00 0.00 C +ATOM 22 HG21 ILE A 2 44.516 -5.666 21.089 1.00 0.00 H +ATOM 23 HG22 ILE A 2 46.148 -5.188 21.725 1.00 0.00 H +ATOM 24 HG23 ILE A 2 46.213 -6.501 20.441 1.00 0.00 H +ATOM 25 CD1 ILE A 2 44.837 -6.338 24.762 1.00 0.00 C +ATOM 26 HD11 ILE A 2 43.908 -5.668 24.416 1.00 0.00 H +ATOM 27 HD12 ILE A 2 44.481 -7.096 25.619 1.00 0.00 H +ATOM 28 HD13 ILE A 2 45.379 -5.509 25.444 1.00 0.00 H +ATOM 29 N GLY A 3 44.161 -9.867 20.749 1.00 0.00 N +ATOM 30 H GLY A 3 44.904 -10.649 21.254 1.00 0.00 H +ATOM 31 CA GLY A 3 43.999 -10.264 19.329 1.00 0.00 C +ATOM 32 HA2 GLY A 3 45.198 -10.196 19.277 1.00 0.00 H +ATOM 33 HA3 GLY A 3 44.008 -10.723 18.220 1.00 0.00 H +ATOM 34 C GLY A 3 42.433 -10.405 19.166 1.00 0.00 C +ATOM 35 O GLY A 3 41.912 -10.061 18.096 1.00 0.00 O +ATOM 36 N ALA A 4 41.862 -10.961 20.191 1.00 0.00 N +ATOM 37 H ALA A 4 42.465 -11.958 20.441 1.00 0.00 H +ATOM 38 CA ALA A 4 40.378 -11.260 20.106 1.00 0.00 C +ATOM 39 HA ALA A 4 40.166 -11.932 19.145 1.00 0.00 H +ATOM 40 C ALA A 4 39.584 -9.950 20.087 1.00 0.00 C +ATOM 41 O ALA A 4 38.676 -9.747 19.278 1.00 0.00 O +ATOM 42 CB ALA A 4 40.061 -12.080 21.350 1.00 0.00 C +ATOM 43 HB1 ALA A 4 39.695 -11.660 22.408 1.00 0.00 H +ATOM 44 HB2 ALA A 4 39.050 -12.651 21.037 1.00 0.00 H +ATOM 45 HB3 ALA A 4 40.749 -13.028 21.606 1.00 0.00 H +ATOM 46 N VAL A 5 39.936 -9.001 20.956 1.00 0.00 N +ATOM 47 H VAL A 5 40.434 -9.436 21.935 1.00 0.00 H +ATOM 48 CA VAL A 5 39.355 -7.658 21.083 1.00 0.00 C +ATOM 49 HA VAL A 5 38.227 -7.901 21.376 1.00 0.00 H +ATOM 50 C VAL A 5 39.536 -6.896 19.795 1.00 0.00 C +ATOM 51 O VAL A 5 38.626 -6.314 19.126 1.00 0.00 O +ATOM 52 CB VAL A 5 39.843 -6.933 22.338 1.00 0.00 C +ATOM 53 HB VAL A 5 40.990 -6.609 22.354 1.00 0.00 H +ATOM 54 CG1 VAL A 5 39.237 -5.519 22.413 1.00 0.00 C +ATOM 55 HG11 VAL A 5 38.720 -4.926 21.518 1.00 0.00 H +ATOM 56 HG12 VAL A 5 38.333 -5.451 23.202 1.00 0.00 H +ATOM 57 HG13 VAL A 5 40.010 -4.710 22.847 1.00 0.00 H +ATOM 58 CG2 VAL A 5 39.745 -7.587 23.653 1.00 0.00 C +ATOM 59 HG21 VAL A 5 39.292 -6.900 24.529 1.00 0.00 H +ATOM 60 HG22 VAL A 5 38.966 -8.493 23.764 1.00 0.00 H +ATOM 61 HG23 VAL A 5 40.731 -7.930 24.237 1.00 0.00 H +ATOM 62 OXT VAL A 5 40.798 -6.914 19.534 1.00 0.00 O +TER 63 VAL A 5 +END diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/2mlt_1to5-movie.dcd b/tests/data/test_implementation_of_lammps_hbond_energies/2mlt_1to5-movie.dcd new file mode 100644 index 00000000..bcfcdc7e Binary files /dev/null and b/tests/data/test_implementation_of_lammps_hbond_energies/2mlt_1to5-movie.dcd differ diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/2mlt_1to5-openmmawsem.pdb b/tests/data/test_implementation_of_lammps_hbond_energies/2mlt_1to5-openmmawsem.pdb new file mode 100644 index 00000000..9223d211 --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/2mlt_1to5-openmmawsem.pdb @@ -0,0 +1,27 @@ +ATOM 1 CA IGL A 1 43.603 -11.488 24.325 1.00 0.00 C +ATOM 2 C IGL A 1 43.264 -10.199 23.553 1.00 0.00 C +ATOM 3 O IGL A 1 42.111 -9.896 23.277 1.00 0.00 O +ATOM 4 N NGP A 2 44.302 -9.461 23.220 1.00 0.00 N +ATOM 5 H NGP A 2 45.234 -9.706 23.444 1.00 0.00 H +ATOM 6 CA NGP A 2 44.200 -8.183 22.475 1.00 0.00 C +ATOM 7 C NGP A 2 43.789 -8.583 21.072 1.00 0.00 C +ATOM 8 O NGP A 2 43.068 -7.904 20.409 1.00 0.00 O +ATOM 9 CB NGP A 2 45.525 -7.320 22.425 1.00 0.00 B +ATOM 10 N IGL A 3 44.271 -9.699 20.648 1.00 0.00 N +ATOM 11 H IGL A 3 44.854 -10.247 21.184 1.00 0.00 H +ATOM 12 CA IGL A 3 43.999 -10.264 19.329 1.00 0.00 C +ATOM 13 C IGL A 3 42.477 -10.433 19.116 1.00 0.00 C +ATOM 14 O IGL A 3 41.912 -10.061 18.096 1.00 0.00 O +ATOM 15 N NGP A 4 41.843 -11.003 20.106 1.00 0.00 N +ATOM 16 H NGP A 4 42.300 -11.303 20.929 1.00 0.00 H +ATOM 17 CA NGP A 4 40.378 -11.260 20.106 1.00 0.00 C +ATOM 18 C NGP A 4 39.591 -9.927 20.070 1.00 0.00 C +ATOM 19 O NGP A 4 38.676 -9.747 19.278 1.00 0.00 O +ATOM 20 CB NGP A 4 40.061 -12.080 21.350 1.00 0.00 B +ATOM 21 N NGP A 5 39.977 -9.009 20.948 1.00 0.00 N +ATOM 22 H NGP A 5 40.716 -9.155 21.587 1.00 0.00 H +ATOM 23 CA NGP A 5 39.355 -7.658 21.083 1.00 0.00 C +ATOM 24 O NGP A 5 38.626 -6.314 19.126 1.00 0.00 O +ATOM 25 CB NGP A 5 39.843 -6.933 22.338 1.00 0.00 B +TER 26 CB NGP A 5 +END diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/2mlt_1to5-ssweight b/tests/data/test_implementation_of_lammps_hbond_energies/2mlt_1to5-ssweight new file mode 100644 index 00000000..8727806e --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/2mlt_1to5-ssweight @@ -0,0 +1,5 @@ +0.0 0.0 +0.0 0.0 +0.0 0.0 +0.0 0.0 +0.0 0.0 diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/2mlt_1to5_cleaned.pdb b/tests/data/test_implementation_of_lammps_hbond_energies/2mlt_1to5_cleaned.pdb new file mode 100644 index 00000000..81a423a1 --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/2mlt_1to5_cleaned.pdb @@ -0,0 +1,66 @@ +REMARK 1 CREATED WITH OPENMM 8.1.1, 2025-12-22 +CRYST1 60.832 38.293 42.211 90.00 90.00 90.00 P 1 1 +ATOM 1 N GLY A 1 42.375 -12.180 24.780 1.00 0.00 N +ATOM 2 H GLY A 1 41.203 -12.267 24.564 1.00 0.00 H +ATOM 3 H2 GLY A 1 42.656 -13.342 24.695 1.00 0.00 H +ATOM 4 H3 GLY A 1 42.346 -11.870 25.939 1.00 0.00 H +ATOM 5 CA GLY A 1 43.603 -11.488 24.325 1.00 0.00 C +ATOM 6 HA2 GLY A 1 44.282 -11.310 25.295 1.00 0.00 H +ATOM 7 HA3 GLY A 1 44.281 -12.169 23.614 1.00 0.00 H +ATOM 8 C GLY A 1 43.288 -10.171 23.615 1.00 0.00 C +ATOM 9 O GLY A 1 42.111 -9.896 23.277 1.00 0.00 O +ATOM 10 N ILE A 2 44.323 -9.391 23.299 1.00 0.00 N +ATOM 11 H ILE A 2 45.382 -9.730 23.721 1.00 0.00 H +ATOM 12 CA ILE A 2 44.200 -8.183 22.475 1.00 0.00 C +ATOM 13 HA ILE A 2 43.357 -7.499 22.957 1.00 0.00 H +ATOM 14 C ILE A 2 43.750 -8.629 21.119 1.00 0.00 C +ATOM 15 O ILE A 2 43.068 -7.904 20.409 1.00 0.00 O +ATOM 16 CB ILE A 2 45.525 -7.320 22.425 1.00 0.00 C +ATOM 17 HB ILE A 2 46.495 -7.948 22.119 1.00 0.00 H +ATOM 18 CG1 ILE A 2 45.924 -6.837 23.820 1.00 0.00 C +ATOM 19 HG12 ILE A 2 46.767 -5.985 23.815 1.00 0.00 H +ATOM 20 HG13 ILE A 2 46.566 -7.648 24.425 1.00 0.00 H +ATOM 21 CG2 ILE A 2 45.555 -6.173 21.386 1.00 0.00 C +ATOM 22 HG21 ILE A 2 44.516 -5.666 21.089 1.00 0.00 H +ATOM 23 HG22 ILE A 2 46.148 -5.188 21.725 1.00 0.00 H +ATOM 24 HG23 ILE A 2 46.213 -6.501 20.441 1.00 0.00 H +ATOM 25 CD1 ILE A 2 44.837 -6.338 24.762 1.00 0.00 C +ATOM 26 HD11 ILE A 2 43.908 -5.668 24.416 1.00 0.00 H +ATOM 27 HD12 ILE A 2 44.481 -7.096 25.619 1.00 0.00 H +ATOM 28 HD13 ILE A 2 45.379 -5.509 25.444 1.00 0.00 H +ATOM 29 N GLY A 3 44.161 -9.867 20.749 1.00 0.00 N +ATOM 30 H GLY A 3 44.904 -10.649 21.254 1.00 0.00 H +ATOM 31 CA GLY A 3 43.999 -10.264 19.329 1.00 0.00 C +ATOM 32 HA2 GLY A 3 45.198 -10.196 19.277 1.00 0.00 H +ATOM 33 HA3 GLY A 3 44.008 -10.723 18.220 1.00 0.00 H +ATOM 34 C GLY A 3 42.433 -10.405 19.166 1.00 0.00 C +ATOM 35 O GLY A 3 41.912 -10.061 18.096 1.00 0.00 O +ATOM 36 N ALA A 4 41.862 -10.961 20.191 1.00 0.00 N +ATOM 37 H ALA A 4 42.465 -11.958 20.441 1.00 0.00 H +ATOM 38 CA ALA A 4 40.378 -11.260 20.106 1.00 0.00 C +ATOM 39 HA ALA A 4 40.166 -11.932 19.145 1.00 0.00 H +ATOM 40 C ALA A 4 39.584 -9.950 20.087 1.00 0.00 C +ATOM 41 O ALA A 4 38.676 -9.747 19.278 1.00 0.00 O +ATOM 42 CB ALA A 4 40.061 -12.080 21.350 1.00 0.00 C +ATOM 43 HB1 ALA A 4 39.695 -11.660 22.408 1.00 0.00 H +ATOM 44 HB2 ALA A 4 39.050 -12.651 21.037 1.00 0.00 H +ATOM 45 HB3 ALA A 4 40.749 -13.028 21.606 1.00 0.00 H +ATOM 46 N VAL A 5 39.936 -9.001 20.956 1.00 0.00 N +ATOM 47 H VAL A 5 40.434 -9.436 21.935 1.00 0.00 H +ATOM 48 CA VAL A 5 39.355 -7.658 21.083 1.00 0.00 C +ATOM 49 HA VAL A 5 38.227 -7.901 21.376 1.00 0.00 H +ATOM 50 C VAL A 5 39.536 -6.896 19.795 1.00 0.00 C +ATOM 51 O VAL A 5 38.626 -6.314 19.126 1.00 0.00 O +ATOM 52 CB VAL A 5 39.843 -6.933 22.338 1.00 0.00 C +ATOM 53 HB VAL A 5 40.990 -6.609 22.354 1.00 0.00 H +ATOM 54 CG1 VAL A 5 39.237 -5.519 22.413 1.00 0.00 C +ATOM 55 HG11 VAL A 5 38.720 -4.926 21.518 1.00 0.00 H +ATOM 56 HG12 VAL A 5 38.333 -5.451 23.202 1.00 0.00 H +ATOM 57 HG13 VAL A 5 40.010 -4.710 22.847 1.00 0.00 H +ATOM 58 CG2 VAL A 5 39.745 -7.587 23.653 1.00 0.00 C +ATOM 59 HG21 VAL A 5 39.292 -6.900 24.529 1.00 0.00 H +ATOM 60 HG22 VAL A 5 38.966 -8.493 23.764 1.00 0.00 H +ATOM 61 HG23 VAL A 5 40.731 -7.930 24.237 1.00 0.00 H +ATOM 62 OXT VAL A 5 40.798 -6.914 19.534 1.00 0.00 O +TER 63 VAL A 5 +END diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/2mlt_1to5_energies.csv b/tests/data/test_implementation_of_lammps_hbond_energies/2mlt_1to5_energies.csv new file mode 100644 index 00000000..ba6b6319 --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/2mlt_1to5_energies.csv @@ -0,0 +1,2 @@ +Step,Beta,Pap,Helical +0.00,0.000000,0.000000,-0.031905 \ No newline at end of file diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/2mlt_frag1-crystal_structure.fasta b/tests/data/test_implementation_of_lammps_hbond_energies/2mlt_frag1-crystal_structure.fasta new file mode 100644 index 00000000..32c6f937 --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/2mlt_frag1-crystal_structure.fasta @@ -0,0 +1,2 @@ +>CRYSTAL_STRUCTURE:A +GIGAVLKVLTTGLP diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/2mlt_frag1-crystal_structure.pdb b/tests/data/test_implementation_of_lammps_hbond_energies/2mlt_frag1-crystal_structure.pdb new file mode 100644 index 00000000..4f7baad3 --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/2mlt_frag1-crystal_structure.pdb @@ -0,0 +1,210 @@ +REMARK 1 CREATED WITH OPENMM 8.1.1, 2025-12-23 +CRYST1 60.832 38.293 42.211 90.00 90.00 90.00 P 1 1 +ATOM 1 N GLY A 1 42.375 -12.180 24.780 1.00 0.00 N +ATOM 2 H GLY A 1 41.348 -11.623 25.042 1.00 0.00 H +ATOM 3 H2 GLY A 1 42.555 -12.690 25.854 1.00 0.00 H +ATOM 4 H3 GLY A 1 42.134 -13.162 24.137 1.00 0.00 H +ATOM 5 CA GLY A 1 43.603 -11.488 24.325 1.00 0.00 C +ATOM 6 HA2 GLY A 1 44.221 -11.213 25.312 1.00 0.00 H +ATOM 7 HA3 GLY A 1 44.301 -12.238 23.709 1.00 0.00 H +ATOM 8 C GLY A 1 43.288 -10.171 23.615 1.00 0.00 C +ATOM 9 O GLY A 1 42.111 -9.896 23.277 1.00 0.00 O +ATOM 10 N ILE A 2 44.323 -9.391 23.299 1.00 0.00 N +ATOM 11 H ILE A 2 45.380 -9.782 23.682 1.00 0.00 H +ATOM 12 CA ILE A 2 44.200 -8.183 22.475 1.00 0.00 C +ATOM 13 HA ILE A 2 43.338 -7.478 22.886 1.00 0.00 H +ATOM 14 C ILE A 2 43.750 -8.629 21.119 1.00 0.00 C +ATOM 15 O ILE A 2 43.068 -7.904 20.409 1.00 0.00 O +ATOM 16 CB ILE A 2 45.525 -7.320 22.425 1.00 0.00 C +ATOM 17 HB ILE A 2 46.450 -7.997 22.088 1.00 0.00 H +ATOM 18 CG1 ILE A 2 45.924 -6.837 23.820 1.00 0.00 C +ATOM 19 HG12 ILE A 2 46.792 -6.010 23.800 1.00 0.00 H +ATOM 20 HG13 ILE A 2 46.531 -7.674 24.425 1.00 0.00 H +ATOM 21 CG2 ILE A 2 45.555 -6.173 21.386 1.00 0.00 C +ATOM 22 HG21 ILE A 2 44.588 -5.494 21.214 1.00 0.00 H +ATOM 23 HG22 ILE A 2 46.339 -5.297 21.634 1.00 0.00 H +ATOM 24 HG23 ILE A 2 46.069 -6.532 20.365 1.00 0.00 H +ATOM 25 CD1 ILE A 2 44.837 -6.338 24.762 1.00 0.00 C +ATOM 26 HD11 ILE A 2 45.139 -5.222 25.094 1.00 0.00 H +ATOM 27 HD12 ILE A 2 44.872 -6.908 25.818 1.00 0.00 H +ATOM 28 HD13 ILE A 2 43.661 -6.128 24.665 1.00 0.00 H +ATOM 29 N GLY A 3 44.161 -9.867 20.749 1.00 0.00 N +ATOM 30 H GLY A 3 45.133 -10.465 21.085 1.00 0.00 H +ATOM 31 CA GLY A 3 43.999 -10.264 19.329 1.00 0.00 C +ATOM 32 HA2 GLY A 3 44.702 -9.646 18.587 1.00 0.00 H +ATOM 33 HA3 GLY A 3 44.390 -11.358 19.035 1.00 0.00 H +ATOM 34 C GLY A 3 42.433 -10.405 19.166 1.00 0.00 C +ATOM 35 O GLY A 3 41.912 -10.061 18.096 1.00 0.00 O +ATOM 36 N ALA A 4 41.862 -10.961 20.191 1.00 0.00 N +ATOM 37 H ALA A 4 42.465 -11.922 20.552 1.00 0.00 H +ATOM 38 CA ALA A 4 40.378 -11.260 20.106 1.00 0.00 C +ATOM 39 HA ALA A 4 40.148 -11.961 19.170 1.00 0.00 H +ATOM 40 C ALA A 4 39.584 -9.950 20.087 1.00 0.00 C +ATOM 41 O ALA A 4 38.676 -9.747 19.278 1.00 0.00 O +ATOM 42 CB ALA A 4 40.061 -12.080 21.350 1.00 0.00 C +ATOM 43 HB1 ALA A 4 39.843 -11.708 22.467 1.00 0.00 H +ATOM 44 HB2 ALA A 4 40.636 -13.124 21.485 1.00 0.00 H +ATOM 45 HB3 ALA A 4 38.960 -12.518 21.142 1.00 0.00 H +ATOM 46 N VAL A 5 39.936 -9.001 20.956 1.00 0.00 N +ATOM 47 H VAL A 5 40.629 -9.354 21.844 1.00 0.00 H +ATOM 48 CA VAL A 5 39.355 -7.658 21.083 1.00 0.00 C +ATOM 49 HA VAL A 5 38.259 -7.965 21.431 1.00 0.00 H +ATOM 50 C VAL A 5 39.536 -6.896 19.795 1.00 0.00 C +ATOM 51 O VAL A 5 38.626 -6.314 19.126 1.00 0.00 O +ATOM 52 CB VAL A 5 39.843 -6.933 22.338 1.00 0.00 C +ATOM 53 HB VAL A 5 40.988 -6.605 22.371 1.00 0.00 H +ATOM 54 CG1 VAL A 5 39.237 -5.519 22.413 1.00 0.00 C +ATOM 55 HG11 VAL A 5 38.051 -5.502 22.584 1.00 0.00 H +ATOM 56 HG12 VAL A 5 39.563 -4.681 21.625 1.00 0.00 H +ATOM 57 HG13 VAL A 5 39.559 -4.865 23.372 1.00 0.00 H +ATOM 58 CG2 VAL A 5 39.745 -7.587 23.653 1.00 0.00 C +ATOM 59 HG21 VAL A 5 39.713 -6.840 24.597 1.00 0.00 H +ATOM 60 HG22 VAL A 5 38.700 -8.144 23.855 1.00 0.00 H +ATOM 61 HG23 VAL A 5 40.504 -8.343 24.190 1.00 0.00 H +ATOM 62 N LEU A 6 40.752 -7.021 19.222 1.00 0.00 N +ATOM 63 H LEU A 6 41.432 -6.456 20.018 1.00 0.00 H +ATOM 64 CA LEU A 6 41.062 -6.432 17.957 1.00 0.00 C +ATOM 65 HA LEU A 6 40.866 -5.262 18.044 1.00 0.00 H +ATOM 66 C LEU A 6 40.230 -6.935 16.870 1.00 0.00 C +ATOM 67 O LEU A 6 39.649 -6.121 16.029 1.00 0.00 O +ATOM 68 CB LEU A 6 42.627 -6.461 17.880 1.00 0.00 C +ATOM 69 HB2 LEU A 6 43.172 -5.759 18.678 1.00 0.00 H +ATOM 70 HB3 LEU A 6 42.971 -7.600 17.910 1.00 0.00 H +ATOM 71 CG LEU A 6 43.125 -6.023 16.524 1.00 0.00 C +ATOM 72 HG LEU A 6 42.903 -6.713 15.576 1.00 0.00 H +ATOM 73 CD1 LEU A 6 42.706 -4.584 16.210 1.00 0.00 C +ATOM 74 HD11 LEU A 6 43.272 -4.298 15.188 1.00 0.00 H +ATOM 75 HD12 LEU A 6 43.196 -3.769 16.945 1.00 0.00 H +ATOM 76 HD13 LEU A 6 41.687 -4.015 15.951 1.00 0.00 H +ATOM 77 CD2 LEU A 6 44.669 -6.152 16.638 1.00 0.00 C +ATOM 78 HD21 LEU A 6 45.189 -5.937 15.574 1.00 0.00 H +ATOM 79 HD22 LEU A 6 45.323 -5.404 17.311 1.00 0.00 H +ATOM 80 HD23 LEU A 6 45.194 -7.216 16.816 1.00 0.00 H +ATOM 81 N LYS A 7 39.981 -8.229 16.721 1.00 0.00 N +ATOM 82 H LYS A 7 40.772 -9.075 16.935 1.00 0.00 H +ATOM 83 CA LYS A 7 39.079 -8.646 15.636 1.00 0.00 C +ATOM 84 HA LYS A 7 39.583 -8.378 14.590 1.00 0.00 H +ATOM 85 C LYS A 7 37.648 -8.063 15.784 1.00 0.00 C +ATOM 86 O LYS A 7 37.031 -7.839 14.731 1.00 0.00 O +ATOM 87 CB LYS A 7 38.854 -10.176 15.616 1.00 0.00 C +ATOM 88 HB2 LYS A 7 37.977 -10.374 14.825 1.00 0.00 H +ATOM 89 HB3 LYS A 7 38.398 -10.663 16.606 1.00 0.00 H +ATOM 90 CG LYS A 7 40.011 -10.993 15.144 1.00 0.00 C +ATOM 91 HG2 LYS A 7 41.158 -10.886 15.464 1.00 0.00 H +ATOM 92 HG3 LYS A 7 40.110 -10.782 13.968 1.00 0.00 H +ATOM 93 CD LYS A 7 39.691 -12.487 15.325 1.00 0.00 C +ATOM 94 HD2 LYS A 7 39.801 -12.898 16.441 1.00 0.00 H +ATOM 95 HD3 LYS A 7 38.586 -12.748 14.951 1.00 0.00 H +ATOM 96 CE LYS A 7 40.599 -13.394 14.493 1.00 0.00 C +ATOM 97 HE2 LYS A 7 41.676 -13.535 14.991 1.00 0.00 H +ATOM 98 HE3 LYS A 7 40.872 -13.049 13.380 1.00 0.00 H +ATOM 99 NZ LYS A 7 39.966 -14.755 14.319 1.00 0.00 N +ATOM 100 HZ1 LYS A 7 39.465 -14.898 13.239 1.00 0.00 H +ATOM 101 HZ2 LYS A 7 40.794 -15.623 14.363 1.00 0.00 H +ATOM 102 HZ3 LYS A 7 39.153 -15.222 15.066 1.00 0.00 H +ATOM 103 N VAL A 8 37.111 -7.988 16.981 1.00 0.00 N +ATOM 104 H VAL A 8 37.403 -8.767 17.821 1.00 0.00 H +ATOM 105 CA VAL A 8 35.792 -7.369 17.211 1.00 0.00 C +ATOM 106 HA VAL A 8 35.091 -8.010 16.491 1.00 0.00 H +ATOM 107 C VAL A 8 35.776 -5.881 16.885 1.00 0.00 C +ATOM 108 O VAL A 8 34.775 -5.402 16.257 1.00 0.00 O +ATOM 109 CB VAL A 8 35.113 -7.600 18.562 1.00 0.00 C +ATOM 110 HB VAL A 8 34.034 -7.086 18.529 1.00 0.00 H +ATOM 111 CG1 VAL A 8 34.774 -9.045 18.851 1.00 0.00 C +ATOM 112 HG11 VAL A 8 33.742 -9.377 18.329 1.00 0.00 H +ATOM 113 HG12 VAL A 8 34.457 -9.332 19.975 1.00 0.00 H +ATOM 114 HG13 VAL A 8 35.415 -10.026 18.593 1.00 0.00 H +ATOM 115 CG2 VAL A 8 35.769 -6.970 19.726 1.00 0.00 C +ATOM 116 HG21 VAL A 8 36.472 -7.757 20.279 1.00 0.00 H +ATOM 117 HG22 VAL A 8 36.066 -5.819 19.842 1.00 0.00 H +ATOM 118 HG23 VAL A 8 34.929 -6.899 20.590 1.00 0.00 H +ATOM 119 N LEU A 9 36.860 -5.176 17.216 1.00 0.00 N +ATOM 120 H LEU A 9 37.858 -5.414 17.783 1.00 0.00 H +ATOM 121 CA LEU A 9 36.899 -3.759 16.725 1.00 0.00 C +ATOM 122 HA LEU A 9 36.033 -3.017 17.052 1.00 0.00 H +ATOM 123 C LEU A 9 36.778 -3.644 15.254 1.00 0.00 C +ATOM 124 O LEU A 9 36.328 -2.551 14.694 1.00 0.00 O +ATOM 125 CB LEU A 9 38.227 -3.088 17.147 1.00 0.00 C +ATOM 126 HB2 LEU A 9 39.189 -3.378 16.504 1.00 0.00 H +ATOM 127 HB3 LEU A 9 38.137 -1.956 16.758 1.00 0.00 H +ATOM 128 CG LEU A 9 38.462 -3.091 18.615 1.00 0.00 C +ATOM 129 HG LEU A 9 38.754 -3.955 19.375 1.00 0.00 H +ATOM 130 CD1 LEU A 9 39.783 -2.288 18.873 1.00 0.00 C +ATOM 131 HD11 LEU A 9 40.856 -2.781 19.080 1.00 0.00 H +ATOM 132 HD12 LEU A 9 39.745 -1.582 19.847 1.00 0.00 H +ATOM 133 HD13 LEU A 9 40.098 -1.424 18.099 1.00 0.00 H +ATOM 134 CD2 LEU A 9 37.265 -2.535 19.351 1.00 0.00 C +ATOM 135 HD21 LEU A 9 37.115 -1.380 19.067 1.00 0.00 H +ATOM 136 HD22 LEU A 9 36.218 -3.088 19.520 1.00 0.00 H +ATOM 137 HD23 LEU A 9 37.478 -2.347 20.522 1.00 0.00 H +ATOM 138 N THR A 10 37.320 -4.627 14.530 1.00 0.00 N +ATOM 139 H THR A 10 37.840 -5.625 14.880 1.00 0.00 H +ATOM 140 CA THR A 10 37.338 -4.508 13.084 1.00 0.00 C +ATOM 141 HA THR A 10 37.440 -3.390 12.679 1.00 0.00 H +ATOM 142 C THR A 10 36.072 -5.022 12.458 1.00 0.00 C +ATOM 143 O THR A 10 35.694 -4.554 11.333 1.00 0.00 O +ATOM 144 CB THR A 10 38.687 -5.179 12.486 1.00 0.00 C +ATOM 145 HB THR A 10 38.867 -4.707 11.403 1.00 0.00 H +ATOM 146 OG1 THR A 10 38.285 -6.538 12.354 1.00 0.00 O +ATOM 147 HG1 THR A 10 39.022 -7.085 11.599 1.00 0.00 H +ATOM 148 CG2 THR A 10 39.877 -5.049 13.451 1.00 0.00 C +ATOM 149 HG21 THR A 10 40.525 -5.741 14.176 1.00 0.00 H +ATOM 150 HG22 THR A 10 40.717 -5.188 12.594 1.00 0.00 H +ATOM 151 HG23 THR A 10 40.027 -3.875 13.642 1.00 0.00 H +ATOM 152 N THR A 11 35.315 -5.870 13.113 1.00 0.00 N +ATOM 153 H THR A 11 35.402 -6.359 14.181 1.00 0.00 H +ATOM 154 CA THR A 11 34.132 -6.405 12.343 1.00 0.00 C +ATOM 155 HA THR A 11 33.776 -5.952 11.299 1.00 0.00 H +ATOM 156 C THR A 11 32.874 -6.299 13.140 1.00 0.00 C +ATOM 157 O THR A 11 31.823 -5.889 12.630 1.00 0.00 O +ATOM 158 CB THR A 11 34.462 -7.925 11.935 1.00 0.00 C +ATOM 159 HB THR A 11 33.509 -8.482 11.478 1.00 0.00 H +ATOM 160 OG1 THR A 11 34.702 -8.591 13.199 1.00 0.00 O +ATOM 161 HG1 THR A 11 34.748 -9.764 13.020 1.00 0.00 H +ATOM 162 CG2 THR A 11 35.695 -7.959 11.047 1.00 0.00 C +ATOM 163 HG21 THR A 11 35.174 -7.957 9.962 1.00 0.00 H +ATOM 164 HG22 THR A 11 36.601 -7.258 10.698 1.00 0.00 H +ATOM 165 HG23 THR A 11 36.212 -9.042 11.053 1.00 0.00 H +ATOM 166 N GLY A 12 32.918 -6.606 14.420 1.00 0.00 N +ATOM 167 H GLY A 12 33.201 -7.715 14.741 1.00 0.00 H +ATOM 168 CA GLY A 12 31.584 -6.595 15.140 1.00 0.00 C +ATOM 169 HA2 GLY A 12 31.429 -7.241 16.136 1.00 0.00 H +ATOM 170 HA3 GLY A 12 30.674 -7.036 14.498 1.00 0.00 H +ATOM 171 C GLY A 12 31.264 -5.168 15.584 1.00 0.00 C +ATOM 172 O GLY A 12 30.060 -4.914 15.603 1.00 0.00 O +ATOM 173 N LEU A 13 32.195 -4.276 15.948 1.00 0.00 N +ATOM 174 H LEU A 13 32.473 -4.884 16.934 1.00 0.00 H +ATOM 175 CA LEU A 13 31.923 -2.919 16.364 1.00 0.00 C +ATOM 176 HA LEU A 13 30.998 -3.094 17.098 1.00 0.00 H +ATOM 177 C LEU A 13 31.251 -2.004 15.324 1.00 0.00 C +ATOM 178 O LEU A 13 30.232 -1.308 15.679 1.00 0.00 O +ATOM 179 CB LEU A 13 33.146 -2.183 17.008 1.00 0.00 C +ATOM 180 HB2 LEU A 13 33.863 -3.073 17.325 1.00 0.00 H +ATOM 181 HB3 LEU A 13 33.501 -1.235 16.375 1.00 0.00 H +ATOM 182 CG LEU A 13 32.913 -1.523 18.351 1.00 0.00 C +ATOM 183 HG LEU A 13 32.879 -2.314 19.248 1.00 0.00 H +ATOM 184 CD1 LEU A 13 33.999 -0.517 18.760 1.00 0.00 C +ATOM 185 HD11 LEU A 13 34.965 -0.295 18.088 1.00 0.00 H +ATOM 186 HD12 LEU A 13 33.658 0.633 18.847 1.00 0.00 H +ATOM 187 HD13 LEU A 13 34.370 -0.681 19.889 1.00 0.00 H +ATOM 188 CD2 LEU A 13 31.587 -0.842 18.531 1.00 0.00 C +ATOM 189 HD21 LEU A 13 31.499 -0.196 19.543 1.00 0.00 H +ATOM 190 HD22 LEU A 13 31.256 0.004 17.748 1.00 0.00 H +ATOM 191 HD23 LEU A 13 30.609 -1.496 18.772 1.00 0.00 H +ATOM 192 N PRO A 14 31.689 -1.979 14.106 1.00 0.00 N +ATOM 193 CA PRO A 14 31.026 -1.278 13.030 1.00 0.00 C +ATOM 194 HA PRO A 14 30.971 -0.101 13.220 1.00 0.00 H +ATOM 195 C PRO A 14 29.521 -1.670 12.857 1.00 0.00 C +ATOM 196 O PRO A 14 28.657 -0.801 12.744 1.00 0.00 O +ATOM 197 CB PRO A 14 31.845 -1.614 11.816 1.00 0.00 C +ATOM 198 HB2 PRO A 14 31.257 -2.227 10.972 1.00 0.00 H +ATOM 199 HB3 PRO A 14 32.036 -0.613 11.183 1.00 0.00 H +ATOM 200 CG PRO A 14 33.118 -2.205 12.303 1.00 0.00 C +ATOM 201 HG2 PRO A 14 33.250 -3.166 11.606 1.00 0.00 H +ATOM 202 HG3 PRO A 14 34.010 -1.511 11.899 1.00 0.00 H +ATOM 203 CD PRO A 14 33.098 -2.363 13.769 1.00 0.00 C +ATOM 204 HD2 PRO A 14 33.564 -3.425 14.021 1.00 0.00 H +ATOM 205 HD3 PRO A 14 33.775 -1.449 14.137 1.00 0.00 H +ATOM 206 OXT PRO A 14 29.767 -2.895 12.875 1.00 0.00 O +TER 207 PRO A 14 +END diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/2mlt_frag1-movie.dcd b/tests/data/test_implementation_of_lammps_hbond_energies/2mlt_frag1-movie.dcd new file mode 100644 index 00000000..c54b2aa6 Binary files /dev/null and b/tests/data/test_implementation_of_lammps_hbond_energies/2mlt_frag1-movie.dcd differ diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/2mlt_frag1-openmmawsem.pdb b/tests/data/test_implementation_of_lammps_hbond_energies/2mlt_frag1-openmmawsem.pdb new file mode 100644 index 00000000..8e33286a --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/2mlt_frag1-openmmawsem.pdb @@ -0,0 +1,79 @@ +ATOM 1 CA IGL A 1 43.603 -11.488 24.325 1.00 0.00 C +ATOM 2 C IGL A 1 43.264 -10.199 23.553 1.00 0.00 C +ATOM 3 O IGL A 1 42.111 -9.896 23.277 1.00 0.00 O +ATOM 4 N NGP A 2 44.302 -9.461 23.220 1.00 0.00 N +ATOM 5 H NGP A 2 45.234 -9.706 23.444 1.00 0.00 H +ATOM 6 CA NGP A 2 44.200 -8.183 22.475 1.00 0.00 C +ATOM 7 C NGP A 2 43.789 -8.583 21.072 1.00 0.00 C +ATOM 8 O NGP A 2 43.068 -7.904 20.409 1.00 0.00 O +ATOM 9 CB NGP A 2 45.525 -7.320 22.425 1.00 0.00 B +ATOM 10 N IGL A 3 44.271 -9.699 20.648 1.00 0.00 N +ATOM 11 H IGL A 3 44.854 -10.247 21.184 1.00 0.00 H +ATOM 12 CA IGL A 3 43.999 -10.264 19.329 1.00 0.00 C +ATOM 13 C IGL A 3 42.477 -10.433 19.116 1.00 0.00 C +ATOM 14 O IGL A 3 41.912 -10.061 18.096 1.00 0.00 O +ATOM 15 N NGP A 4 41.843 -11.003 20.106 1.00 0.00 N +ATOM 16 H NGP A 4 42.300 -11.303 20.929 1.00 0.00 H +ATOM 17 CA NGP A 4 40.378 -11.260 20.106 1.00 0.00 C +ATOM 18 C NGP A 4 39.591 -9.927 20.070 1.00 0.00 C +ATOM 19 O NGP A 4 38.676 -9.747 19.278 1.00 0.00 O +ATOM 20 CB NGP A 4 40.061 -12.080 21.350 1.00 0.00 B +ATOM 21 N NGP A 5 39.977 -9.009 20.948 1.00 0.00 N +ATOM 22 H NGP A 5 40.716 -9.155 21.587 1.00 0.00 H +ATOM 23 CA NGP A 5 39.355 -7.658 21.083 1.00 0.00 C +ATOM 24 C NGP A 5 39.522 -6.938 19.719 1.00 0.00 C +ATOM 25 O NGP A 5 38.626 -6.314 19.126 1.00 0.00 O +ATOM 26 CB NGP A 5 39.843 -6.933 22.338 1.00 0.00 B +ATOM 27 N NGP A 6 40.693 -7.047 19.250 1.00 0.00 N +ATOM 28 H NGP A 6 41.417 -7.550 19.729 1.00 0.00 H +ATOM 29 CA NGP A 6 41.062 -6.432 17.957 1.00 0.00 C +ATOM 30 C NGP A 6 40.142 -6.853 16.792 1.00 0.00 C +ATOM 31 O NGP A 6 39.649 -6.121 16.029 1.00 0.00 O +ATOM 32 CB NGP A 6 42.627 -6.461 17.880 1.00 0.00 B +ATOM 33 N NGP A 7 39.932 -8.047 16.685 1.00 0.00 N +ATOM 34 H NGP A 7 40.331 -8.638 17.301 1.00 0.00 H +ATOM 35 CA NGP A 7 39.079 -8.646 15.636 1.00 0.00 C +ATOM 36 C NGP A 7 37.648 -8.086 15.716 1.00 0.00 C +ATOM 37 O NGP A 7 37.031 -7.839 14.731 1.00 0.00 O +ATOM 38 CB NGP A 7 38.854 -10.176 15.616 1.00 0.00 B +ATOM 39 N NGP A 8 37.150 -7.899 16.913 1.00 0.00 N +ATOM 40 H NGP A 8 37.650 -8.099 17.708 1.00 0.00 H +ATOM 41 CA NGP A 8 35.792 -7.369 17.211 1.00 0.00 C +ATOM 42 C NGP A 8 35.726 -5.888 16.790 1.00 0.00 C +ATOM 43 O NGP A 8 34.775 -5.402 16.257 1.00 0.00 O +ATOM 44 CB NGP A 8 35.113 -7.600 18.562 1.00 0.00 B +ATOM 45 N NGP A 9 36.761 -5.197 17.048 1.00 0.00 N +ATOM 46 H NGP A 9 37.529 -5.589 17.478 1.00 0.00 H +ATOM 47 CA NGP A 9 36.899 -3.759 16.725 1.00 0.00 C +ATOM 48 C NGP A 9 36.819 -3.547 15.216 1.00 0.00 C +ATOM 49 O NGP A 9 36.328 -2.551 14.694 1.00 0.00 O +ATOM 50 CB NGP A 9 38.227 -3.088 17.147 1.00 0.00 B +ATOM 51 N NGP A 10 37.315 -4.511 14.543 1.00 0.00 N +ATOM 52 H NGP A 10 37.713 -5.315 14.965 1.00 0.00 H +ATOM 53 CA NGP A 10 37.338 -4.508 13.084 1.00 0.00 C +ATOM 54 C NGP A 10 36.056 -4.969 12.347 1.00 0.00 C +ATOM 55 O NGP A 10 35.694 -4.554 11.333 1.00 0.00 O +ATOM 56 CB NGP A 10 38.687 -5.179 12.486 1.00 0.00 B +ATOM 57 N NGP A 11 35.391 -5.834 12.890 1.00 0.00 N +ATOM 58 H NGP A 11 35.684 -6.169 13.708 1.00 0.00 H +ATOM 59 CA NGP A 11 34.132 -6.405 12.343 1.00 0.00 C +ATOM 60 C NGP A 11 32.791 -6.284 13.093 1.00 0.00 C +ATOM 61 O NGP A 11 31.823 -5.889 12.630 1.00 0.00 O +ATOM 62 CB NGP A 11 34.462 -7.925 11.935 1.00 0.00 B +ATOM 63 N IGL A 12 32.772 -6.635 14.257 1.00 0.00 N +ATOM 64 H IGL A 12 33.554 -6.954 14.631 1.00 0.00 H +ATOM 65 CA IGL A 12 31.584 -6.595 15.140 1.00 0.00 C +ATOM 66 C IGL A 12 31.174 -5.191 15.577 1.00 0.00 C +ATOM 67 O IGL A 12 30.060 -4.914 15.603 1.00 0.00 O +ATOM 68 N NGP A 13 32.107 -4.323 15.915 1.00 0.00 N +ATOM 69 H NGP A 13 33.007 -4.547 15.894 1.00 0.00 H +ATOM 70 CA NGP A 13 31.923 -2.919 16.364 1.00 0.00 C +ATOM 71 C NGP A 13 31.169 -2.016 15.360 1.00 0.00 C +ATOM 72 O NGP A 13 30.232 -1.308 15.679 1.00 0.00 O +ATOM 73 CB NGP A 13 33.146 -2.183 17.008 1.00 0.00 B +ATOM 74 N IPR A 14 31.608 -2.065 14.147 1.00 0.00 N +ATOM 75 CA IPR A 14 31.026 -1.278 13.030 1.00 0.00 C +ATOM 76 O IPR A 14 28.657 -0.801 12.744 1.00 0.00 O +ATOM 77 CB IPR A 14 31.845 -1.614 11.816 1.00 0.00 B +TER 78 CB IPR A 14 +END diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/2mlt_frag1-ssweight b/tests/data/test_implementation_of_lammps_hbond_energies/2mlt_frag1-ssweight new file mode 100644 index 00000000..a73aeb65 --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/2mlt_frag1-ssweight @@ -0,0 +1,14 @@ +0.0 0.0 +0.0 0.0 +1.0 0.0 +1.0 0.0 +1.0 0.0 +1.0 0.0 +1.0 0.0 +1.0 0.0 +1.0 0.0 +1.0 0.0 +1.0 0.0 +0.0 0.0 +0.0 0.0 +0.0 0.0 diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/2mlt_frag1_energies.csv b/tests/data/test_implementation_of_lammps_hbond_energies/2mlt_frag1_energies.csv new file mode 100644 index 00000000..511f83a4 --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/2mlt_frag1_energies.csv @@ -0,0 +1,2 @@ +Step,Beta,Pap,Helical +0.00,0.000000,0.000000,-2.032375 diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/lammps_setup_scripts/VectorAlgebra.pyc b/tests/data/test_implementation_of_lammps_hbond_energies/lammps_setup_scripts/VectorAlgebra.pyc deleted file mode 100644 index c1515273..00000000 Binary files a/tests/data/test_implementation_of_lammps_hbond_energies/lammps_setup_scripts/VectorAlgebra.pyc and /dev/null differ diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_1to5/2mlt_1to5.coord b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_1to5/2mlt_1to5.coord new file mode 100644 index 00000000..748a827f --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_1to5/2mlt_1to5.coord @@ -0,0 +1,25 @@ +1 1 N 42.375 -12.18000031 24.78000069 N +2 1 C 43.60300064 -11.48799992 24.32500076 C-Alpha +3 1 C 43.2879982 -10.17099953 23.61499977 C-Prime +4 1 O 42.11100006 -9.89599991 23.27700043 O +5 1 H 43.68213344 -10.74355373 25.67078599 H-Beta +6 1 N 44.32300186 -9.39099979 23.29899979 N +7 1 C 44.20000076 -8.18299961 22.47500038 C-Alpha +8 1 C 43.75 -8.62899971 21.11899948 C-Prime +9 1 O 43.06800079 -7.90399981 20.4090004 O +10 1 C 45.52500153 -7.32000017 22.42499924 C-Beta +11 1 N 44.1609993 -9.86699963 20.74900055 N +12 1 C 43.99900055 -10.26399994 19.32900047 C-Alpha +13 1 C 42.43299866 -10.40499973 19.16600037 C-Prime +14 1 O 41.91199875 -10.06099987 18.09600067 O +15 1 H 43.90753259 -8.78081694 18.9247706 H-Beta +16 1 N 41.86199951 -10.96100044 20.19099998 N +17 1 C 40.37799835 -11.26000023 20.1060009 C-Alpha +18 1 C 39.58399963 -9.94999981 20.08699989 C-Prime +19 1 O 38.67599869 -9.74699974 19.27799988 O +20 1 C 40.06100082 -12.07999992 21.35000038 C-Beta +21 1 N 39.93600082 -9.0010004 20.95599937 N +22 1 C 39.35499954 -7.65799999 21.08300018 C-Alpha +23 1 C 39.5359993 -6.89599991 19.79500008 C-Prime +24 1 O 38.62599945 -6.31400013 19.12599945 O +25 1 C 39.8429985 -6.93300009 22.33799934 C-Beta diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_1to5/2mlt_1to5.in b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_1to5/2mlt_1to5.in new file mode 100644 index 00000000..0aa0fdc2 --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_1to5/2mlt_1to5.in @@ -0,0 +1,52 @@ +# 3d protein simulation + +units real + +timestep 2 + +dimension 3 + +boundary s s s +#boundary p p p + +neighbor 10 bin +neigh_modify delay 5 + +atom_modify sort 0 0.0 + +special_bonds fene + +atom_style awsemmd + +bond_style harmonic + +pair_style vexcluded 2 3.5 3.5 + +read_data data.2mlt_1to5 + +pair_coeff * * 0.0 +pair_coeff 1 1 20.0 3.5 4.5 +pair_coeff 1 4 20.0 3.5 4.5 +pair_coeff 4 4 20.0 3.5 4.5 +pair_coeff 3 3 20.0 3.5 3.5 + + +velocity all create 300.0 2349852 + +group alpha_carbons id 1 4 7 10 13 + +group beta_atoms id 3 6 9 12 15 + +group oxygens id 2 5 8 11 14 + + +fix 1 all nvt temp 300.0 300.0 100.0 +fix 2 alpha_carbons backbone beta_atoms oxygens fix_backbone_coeff.data 2mlt_1to5.seq + +thermo 1000 +dump 1 all atom 1000 dump.lammpstrj + +dump_modify 1 sort id + +reset_timestep 0 +run 0 diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_1to5/2mlt_1to5.pdb b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_1to5/2mlt_1to5.pdb new file mode 100644 index 00000000..74676c80 --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_1to5/2mlt_1to5.pdb @@ -0,0 +1,64 @@ +REMARK 1 CREATED WITH OPENMM 8.1.1, 2025-12-20 +CRYST1 60.832 38.293 42.211 90.00 90.00 90.00 P 1 1 +ATOM 1 N GLY A 1 42.375 -12.180 24.780 1.00 0.00 N +ATOM 2 H GLY A 1 41.203 -12.267 24.564 1.00 0.00 H +ATOM 3 H2 GLY A 1 42.656 -13.342 24.695 1.00 0.00 H +ATOM 4 H3 GLY A 1 42.346 -11.870 25.939 1.00 0.00 H +ATOM 5 CA GLY A 1 43.603 -11.488 24.325 1.00 0.00 C +ATOM 6 HA2 GLY A 1 44.282 -11.310 25.295 1.00 0.00 H +ATOM 7 HA3 GLY A 1 44.281 -12.169 23.614 1.00 0.00 H +ATOM 8 C GLY A 1 43.288 -10.171 23.615 1.00 0.00 C +ATOM 9 O GLY A 1 42.111 -9.896 23.277 1.00 0.00 O +ATOM 10 N ILE A 2 44.323 -9.391 23.299 1.00 0.00 N +ATOM 11 H ILE A 2 45.382 -9.730 23.721 1.00 0.00 H +ATOM 12 CA ILE A 2 44.200 -8.183 22.475 1.00 0.00 C +ATOM 13 HA ILE A 2 43.357 -7.499 22.957 1.00 0.00 H +ATOM 14 C ILE A 2 43.750 -8.629 21.119 1.00 0.00 C +ATOM 15 O ILE A 2 43.068 -7.904 20.409 1.00 0.00 O +ATOM 16 CB ILE A 2 45.525 -7.320 22.425 1.00 0.00 C +ATOM 17 HB ILE A 2 46.495 -7.948 22.119 1.00 0.00 H +ATOM 18 CG1 ILE A 2 45.924 -6.837 23.820 1.00 0.00 C +ATOM 19 HG12 ILE A 2 46.767 -5.985 23.815 1.00 0.00 H +ATOM 20 HG13 ILE A 2 46.566 -7.648 24.425 1.00 0.00 H +ATOM 21 CG2 ILE A 2 45.555 -6.173 21.386 1.00 0.00 C +ATOM 22 HG21 ILE A 2 44.516 -5.666 21.089 1.00 0.00 H +ATOM 23 HG22 ILE A 2 46.148 -5.188 21.725 1.00 0.00 H +ATOM 24 HG23 ILE A 2 46.213 -6.501 20.441 1.00 0.00 H +ATOM 25 CD1 ILE A 2 44.837 -6.338 24.762 1.00 0.00 C +ATOM 26 HD11 ILE A 2 43.908 -5.668 24.416 1.00 0.00 H +ATOM 27 HD12 ILE A 2 44.481 -7.096 25.619 1.00 0.00 H +ATOM 28 HD13 ILE A 2 45.379 -5.509 25.444 1.00 0.00 H +ATOM 29 N GLY A 3 44.161 -9.867 20.749 1.00 0.00 N +ATOM 30 H GLY A 3 44.904 -10.649 21.254 1.00 0.00 H +ATOM 31 CA GLY A 3 43.999 -10.264 19.329 1.00 0.00 C +ATOM 32 HA2 GLY A 3 45.198 -10.196 19.277 1.00 0.00 H +ATOM 33 HA3 GLY A 3 44.008 -10.723 18.220 1.00 0.00 H +ATOM 34 C GLY A 3 42.433 -10.405 19.166 1.00 0.00 C +ATOM 35 O GLY A 3 41.912 -10.061 18.096 1.00 0.00 O +ATOM 36 N ALA A 4 41.862 -10.961 20.191 1.00 0.00 N +ATOM 37 H ALA A 4 42.465 -11.958 20.441 1.00 0.00 H +ATOM 38 CA ALA A 4 40.378 -11.260 20.106 1.00 0.00 C +ATOM 39 HA ALA A 4 40.166 -11.932 19.145 1.00 0.00 H +ATOM 40 C ALA A 4 39.584 -9.950 20.087 1.00 0.00 C +ATOM 41 O ALA A 4 38.676 -9.747 19.278 1.00 0.00 O +ATOM 42 CB ALA A 4 40.061 -12.080 21.350 1.00 0.00 C +ATOM 43 HB1 ALA A 4 39.695 -11.660 22.408 1.00 0.00 H +ATOM 44 HB2 ALA A 4 39.050 -12.651 21.037 1.00 0.00 H +ATOM 45 HB3 ALA A 4 40.749 -13.028 21.606 1.00 0.00 H +ATOM 46 N VAL A 5 39.936 -9.001 20.956 1.00 0.00 N +ATOM 47 H VAL A 5 40.434 -9.436 21.935 1.00 0.00 H +ATOM 48 CA VAL A 5 39.355 -7.658 21.083 1.00 0.00 C +ATOM 49 HA VAL A 5 38.227 -7.901 21.376 1.00 0.00 H +ATOM 50 C VAL A 5 39.536 -6.896 19.795 1.00 0.00 C +ATOM 51 O VAL A 5 38.626 -6.314 19.126 1.00 0.00 O +ATOM 52 CB VAL A 5 39.843 -6.933 22.338 1.00 0.00 C +ATOM 53 HB VAL A 5 40.990 -6.609 22.354 1.00 0.00 H +ATOM 54 CG1 VAL A 5 39.237 -5.519 22.413 1.00 0.00 C +ATOM 55 HG11 VAL A 5 38.720 -4.926 21.518 1.00 0.00 H +ATOM 56 HG12 VAL A 5 38.333 -5.451 23.202 1.00 0.00 H +ATOM 57 HG13 VAL A 5 40.010 -4.710 22.847 1.00 0.00 H +ATOM 58 CG2 VAL A 5 39.745 -7.587 23.653 1.00 0.00 C +ATOM 59 HG21 VAL A 5 39.292 -6.900 24.529 1.00 0.00 H +ATOM 60 HG22 VAL A 5 38.966 -8.493 23.764 1.00 0.00 H +ATOM 61 HG23 VAL A 5 40.731 -7.930 24.237 1.00 0.00 H +END diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_1to5/2mlt_1to5.seq b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_1to5/2mlt_1to5.seq new file mode 100644 index 00000000..94062260 --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_1to5/2mlt_1to5.seq @@ -0,0 +1 @@ +GIGAV diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_1to5/anti_HB b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_1to5/anti_HB new file mode 100644 index 00000000..c43ad083 --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_1to5/anti_HB @@ -0,0 +1,41 @@ + 0.00000 -1.80130 0.00000 0.00000 0.00000 0.00000 0.00000 0.88204 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.67395 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 1.19422 0.00000 0.82412 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.50158 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.89208 0.00000 0.00000 0.99199 0.67662 0.00000 0.00000 0.00000 -1.13044 0.00000 1.02639 0.00000 0.00000 0.98118 0.00000 0.00000 0.00000 0.00000 + 0.00000 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+-0.05899 -0.36672 +-0.10044 0.19480 + 0.42645 -1.00000 + 0.15157 -0.94841 + 0.43719 1.00000 + 0.21090 -0.44608 + 0.59308 0.37531 + 0.73327 0.86844 diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_1to5/lammps_movie.dcd b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_1to5/lammps_movie.dcd new file mode 100644 index 00000000..bcfcdc7e Binary files /dev/null and b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_1to5/lammps_movie.dcd differ diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_1to5/lammps_movie.pdb b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_1to5/lammps_movie.pdb new file mode 100644 index 00000000..7fc407bc --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_1to5/lammps_movie.pdb @@ -0,0 +1,27 @@ +MODEL 1 +ATOM 1 CA GLY A 1 43.603 -11.488 24.325 1.00 0.00 C +ATOM 2 C GLY A 1 43.264 -10.199 23.553 1.00 0.00 C +ATOM 3 O GLY A 1 42.111 -9.896 23.277 1.00 0.00 O +ATOM 4 N ILE A 2 44.303 -9.461 23.22 1.00 0.00 N +ATOM 5 H ILE A 2 45.234 -9.706 23.444 1.00 0.00 H +ATOM 6 CA ILE A 2 44.2 -8.183 22.475 1.00 0.00 C +ATOM 7 C ILE A 2 43.789 -8.583 21.072 1.00 0.00 C +ATOM 8 O ILE A 2 43.068 -7.904 20.409 1.00 0.00 O +ATOM 9 CB ILE A 2 45.525 -7.32 22.425 1.00 0.00 C +ATOM 10 N GLY A 3 44.271 -9.699 20.648 1.00 0.00 N +ATOM 11 H GLY A 3 44.854 -10.247 21.184 1.00 0.00 H +ATOM 12 CA GLY A 3 43.999 -10.264 19.329 1.00 0.00 C +ATOM 13 C GLY A 3 42.477 -10.433 19.116 1.00 0.00 C +ATOM 14 O GLY A 3 41.912 -10.061 18.096 1.00 0.00 O +ATOM 15 N ALA A 4 41.843 -11.003 20.106 1.00 0.00 N +ATOM 16 H ALA A 4 42.3 -11.303 20.929 1.00 0.00 H +ATOM 17 CA ALA A 4 40.378 -11.26 20.106 1.00 0.00 C +ATOM 18 C ALA A 4 39.591 -9.927 20.07 1.00 0.00 C +ATOM 19 O ALA A 4 38.676 -9.747 19.278 1.00 0.00 O +ATOM 20 CB ALA A 4 40.061 -12.08 21.35 1.00 0.00 C +ATOM 21 N VAL A 5 39.977 -9.009 20.948 1.00 0.00 N +ATOM 22 H VAL A 5 40.716 -9.155 21.587 1.00 0.00 H +ATOM 23 CA VAL A 5 39.355 -7.658 21.083 1.00 0.00 C +ATOM 24 O VAL A 5 38.626 -6.314 19.126 1.00 0.00 O +ATOM 25 CB VAL A 5 39.843 -6.933 22.338 1.00 0.00 C +ENDMDL diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_1to5/lammps_movie.psf b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_1to5/lammps_movie.psf new file mode 100644 index 00000000..26fc5b4d --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_1to5/lammps_movie.psf @@ -0,0 +1,38 @@ +PSF + + 0 !NTITLE + + 25 !NATOM + 1 PROT 1 GLY CA C 0 1 0 + 2 PROT 1 GLY C C 0 1 0 + 3 PROT 1 GLY O O 0 1 0 + 4 PROT 2 ILE N N 0 1 0 + 5 PROT 2 ILE H H 0 1 0 + 6 PROT 2 ILE CA C 0 1 0 + 7 PROT 2 ILE C C 0 1 0 + 8 PROT 2 ILE O O 0 1 0 + 9 PROT 2 ILE CB C 0 1 0 + 10 PROT 3 GLY N N 0 1 0 + 11 PROT 3 GLY H H 0 1 0 + 12 PROT 3 GLY CA C 0 1 0 + 13 PROT 3 GLY C C 0 1 0 + 14 PROT 3 GLY O O 0 1 0 + 15 PROT 4 ALA N N 0 1 0 + 16 PROT 4 ALA H H 0 1 0 + 17 PROT 4 ALA CA C 0 1 0 + 18 PROT 4 ALA C C 0 1 0 + 19 PROT 4 ALA O O 0 1 0 + 20 PROT 4 ALA CB C 0 1 0 + 21 PROT 5 VAL N N 0 1 0 + 22 PROT 5 VAL H H 0 1 0 + 23 PROT 5 VAL CA C 0 1 0 + 24 PROT 5 VAL O O 0 1 0 + 25 PROT 5 VAL CB C 0 1 0 + + 21 !NBOND + 1 2 2 3 1 4 2 5 + 5 7 7 8 8 9 7 10 + 8 11 11 13 13 14 14 15 + 13 16 14 17 17 19 19 20 + 20 21 19 22 20 23 23 25 + 25 27 \ No newline at end of file diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_1to5/lammps_stdout.txt b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_1to5/lammps_stdout.txt new file mode 100644 index 00000000..1fa722a5 --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_1to5/lammps_stdout.txt @@ -0,0 +1,101 @@ +LAMMPS (29 Aug 2024 - Update 1) +Reading data file ... + orthogonal box = (-200 -200 -200) to (200 200 200) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 15 atoms + scanning bonds ... + 3 = max bonds/atom + orthogonal box = (-200.04 -200.04 -200.04) to (200.04 200.04 200.04) + 1 by 1 by 1 MPI processor grid + reading bonds ... + 18 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 1 1 + 5 = max # of 1-2 neighbors + 5 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.018 seconds +5 atoms in group alpha_carbons +5 atoms in group beta_atoms +5 atoms in group oxygens +Chain flag on +Chi flag on +Rama flag on +Rama_P flag on +SSWeight flag on +ABC flag on +Dssp_Hdrgn flag on +P_AP flag on +Water flag on +Burial flag on +Helix flag on + +Fix backbone Pair List cutoff 15.0000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: +- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419 +The log file lists these citations in BibTeX format. + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Generated 0 of 10 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 5 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14.5 + ghost atom cutoff = 25 + binsize = 7.25, bins = 1 1 2 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair vexcluded, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) fix backbone, perpetual + attributes: half, newton on, cut 25 + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:1202) +Setting up Verlet run ... + Unit style : real + Current step : 0 + Time step : 2 +se[j_resno]: V +xn[j]: 39.9773 -9.00925 20.9482 +xh[j]: 40.7164 -9.15472 21.5875 +Per MPI rank memory allocation (min/avg/max) = 7.204 | 7.204 | 7.204 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 0 300 0.46503536 80.448351 93.432789 -129172.68 312.31168 +Loop time of 8.09e-07 on 1 procs for 0 steps with 15 atoms + +123.6% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Bond | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 8.09e-07 | | |100.00 + +Nlocal: 15 ave 15 max 15 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 87 ave 87 max 87 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 87 +Ave neighs/atom = 5.8 +Ave special neighs/atom = 2.4 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_1to5/log.lammps b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_1to5/log.lammps new file mode 100644 index 00000000..7062e82d --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_1to5/log.lammps @@ -0,0 +1,156 @@ +LAMMPS (29 Aug 2024 - Update 1) +# 3d protein simulation + +units real + +timestep 2 + +dimension 3 + +boundary s s s +#boundary p p p + +neighbor 10 bin +neigh_modify delay 5 + +atom_modify sort 0 0.0 + +special_bonds fene + +atom_style awsemmd + +bond_style harmonic + +pair_style vexcluded 2 3.5 3.5 + +read_data data.2mlt_1to5 +Reading data file ... + orthogonal box = (-200 -200 -200) to (200 200 200) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 15 atoms + scanning bonds ... + 3 = max bonds/atom + orthogonal box = (-200.04 -200.04 -200.04) to (200.04 200.04 200.04) + 1 by 1 by 1 MPI processor grid + reading bonds ... + 18 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 1 1 + 5 = max # of 1-2 neighbors + 5 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.018 seconds + +pair_coeff * * 0.0 +pair_coeff 1 1 20.0 3.5 4.5 +pair_coeff 1 4 20.0 3.5 4.5 +pair_coeff 4 4 20.0 3.5 4.5 +pair_coeff 3 3 20.0 3.5 3.5 + + +velocity all create 300.0 2349852 + +group alpha_carbons id 1 4 7 10 13 +5 atoms in group alpha_carbons + +group beta_atoms id 3 6 9 12 15 +5 atoms in group beta_atoms + +group oxygens id 2 5 8 11 14 +5 atoms in group oxygens + + +fix 1 all nvt temp 300.0 300.0 100.0 +fix 2 alpha_carbons backbone beta_atoms oxygens fix_backbone_coeff.data 2mlt_1to5.seq +Chain flag on +Chi flag on +Rama flag on +Rama_P flag on +SSWeight flag on +ABC flag on +Dssp_Hdrgn flag on +P_AP flag on +Water flag on +Burial flag on +Helix flag on + +Fix backbone Pair List cutoff 15.0000 + +thermo 1000 +dump 1 all atom 1000 dump.lammpstrj + +dump_modify 1 sort id + +reset_timestep 0 +run 0 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419 + +@Article{Gissinger24, + author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor}, + title = {Type Label Framework for Bonded Force Fields in LAMMPS}, + journal = {J. Phys. Chem. B}, + year = 2024, + volume = 128, + number = 13, + pages = {3282–-3297} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Generated 0 of 10 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 5 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14.5 + ghost atom cutoff = 25 + binsize = 7.25, bins = 1 1 2 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair vexcluded, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) fix backbone, perpetual + attributes: half, newton on, cut 25 + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:1202) +Per MPI rank memory allocation (min/avg/max) = 7.204 | 7.204 | 7.204 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 0 300 0.46503536 80.448351 93.432789 -129172.68 312.31168 +Loop time of 8.09e-07 on 1 procs for 0 steps with 15 atoms + +123.6% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Bond | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 8.09e-07 | | |100.00 + +Nlocal: 15 ave 15 max 15 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 87 ave 87 max 87 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 87 +Ave neighs/atom = 5.8 +Ave special neighs/atom = 2.4 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_1to5/para_HB 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b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/2mlt_frag1.coord new file mode 100644 index 00000000..f9f1c382 --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/2mlt_frag1.coord @@ -0,0 +1,70 @@ +1 1 N 42.375 -12.18000031 24.78000069 N +2 1 C 43.60300064 -11.48799992 24.32500076 C-Alpha +3 1 C 43.2879982 -10.17099953 23.61499977 C-Prime +4 1 O 42.11100006 -9.89599991 23.27700043 O +5 1 H 43.68213344 -10.74355373 25.67078599 H-Beta +6 1 N 44.32300186 -9.39099979 23.29899979 N +7 1 C 44.20000076 -8.18299961 22.47500038 C-Alpha +8 1 C 43.75 -8.62899971 21.11899948 C-Prime +9 1 O 43.06800079 -7.90399981 20.4090004 O +10 1 C 45.52500153 -7.32000017 22.42499924 C-Beta +11 1 N 44.1609993 -9.86699963 20.74900055 N +12 1 C 43.99900055 -10.26399994 19.32900047 C-Alpha +13 1 C 42.43299866 -10.40499973 19.16600037 C-Prime +14 1 O 41.91199875 -10.06099987 18.09600067 O +15 1 H 43.90753259 -8.78081694 18.9247706 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37.11100006 -7.98799992 16.9810009 N +37 1 C 35.79199982 -7.36899996 17.21100044 C-Alpha +38 1 C 35.77600098 -5.88100004 16.88500023 C-Prime +39 1 O 34.77500153 -5.40199995 16.25699997 O +40 1 C 35.11299896 -7.5999999 18.56200027 C-Beta +41 1 N 36.86000061 -5.17600012 17.2159996 N +42 1 C 36.89899826 -3.75900006 16.72500038 C-Alpha +43 1 C 36.77799988 -3.64400005 15.25399971 C-Prime +44 1 O 36.32799911 -2.55100012 14.69400024 O +45 1 C 38.22700119 -3.08800006 17.14699936 C-Beta +46 1 N 37.31999969 -4.62699986 14.52999973 N +47 1 C 37.33800125 -4.5079999 13.08399963 C-Alpha +48 1 C 36.0719986 -5.02199984 12.45800018 C-Prime +49 1 O 35.69400024 -4.5539999 11.33300018 O +50 1 C 38.68700027 -5.1789999 12.48600006 C-Beta +51 1 N 35.31499863 -5.86999989 13.11299992 N +52 1 C 34.13199997 -6.40500021 12.34300041 C-Alpha +53 1 C 32.87400055 -6.29899979 13.14000034 C-Prime +54 1 O 31.82299995 -5.88899994 12.63000011 O +55 1 C 34.4620018 -7.92500019 11.93500042 C-Beta +56 1 N 32.91799927 -6.60599995 14.42000008 N +57 1 C 31.58399963 -6.59499979 15.14000034 C-Alpha +58 1 C 31.26399994 -5.16800022 15.58399963 C-Prime +59 1 O 30.05999947 -4.91400003 15.60299969 O +60 1 H 30.86425559 -6.34027362 13.80258377 H-Beta +61 1 N 32.19499969 -4.27600002 15.94799995 N +62 1 C 31.92300034 -2.91899991 16.36400032 C-Alpha +63 1 C 31.25099945 -2.00399995 15.32400036 C-Prime +64 1 O 30.23200035 -1.30799997 15.6789999 O +65 1 C 33.14599991 -2.18300009 17.00799942 C-Beta +66 1 N 31.68899918 -1.97899997 14.10599995 N +67 1 C 31.02599907 -1.278 13.02999973 C-Alpha +68 1 C 29.52099991 -1.66999996 12.85700035 C-Prime +69 1 O 28.65699959 -0.801 12.74400043 O +70 1 C 31.84499931 -1.61399996 11.81599998 C-Beta diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/2mlt_frag1.in b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/2mlt_frag1.in new file mode 100644 index 00000000..363129be --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/2mlt_frag1.in @@ -0,0 +1,52 @@ +# 3d protein simulation + +units real + +timestep 2 + +dimension 3 + +boundary s s s +#boundary p p p + +neighbor 10 bin +neigh_modify delay 5 + +atom_modify sort 0 0.0 + +special_bonds fene + +atom_style awsemmd + +bond_style harmonic + +pair_style vexcluded 2 3.5 3.5 + +read_data data.2mlt_frag1 + +pair_coeff * * 0.0 +pair_coeff 1 1 20.0 3.5 4.5 +pair_coeff 1 4 20.0 3.5 4.5 +pair_coeff 4 4 20.0 3.5 4.5 +pair_coeff 3 3 20.0 3.5 3.5 + + +velocity all create 300.0 2349852 + +group alpha_carbons id 1 4 7 10 13 16 19 22 25 28 31 34 37 40 + +group beta_atoms id 3 6 9 12 15 18 21 24 27 30 33 36 39 42 + +group oxygens id 2 5 8 11 14 17 20 23 26 29 32 35 38 41 + + +fix 1 all nvt temp 300.0 300.0 100.0 +fix 2 alpha_carbons backbone beta_atoms oxygens fix_backbone_coeff.data 2mlt_frag1.seq + +thermo 1000 +dump 1 all atom 1000 dump.lammpstrj + +dump_modify 1 sort id + +reset_timestep 0 +run 0 diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/2mlt_frag1.pdb b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/2mlt_frag1.pdb new file mode 100644 index 00000000..6913f62a --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/2mlt_frag1.pdb @@ -0,0 +1,104 @@ +CRYST1 60.832 38.293 42.211 90.00 90.00 90.00 C 2 2 21 16 +ORIGX1 1.000000 0.000000 0.000000 0.00000 +ORIGX2 0.000000 1.000000 0.000000 0.00000 +ORIGX3 0.000000 0.000000 1.000000 0.00000 +SCALE1 0.016439 0.000000 0.000000 0.00000 +SCALE2 0.000000 0.026114 0.000000 0.00000 +SCALE3 0.000000 0.000000 0.023691 0.00000 +MTRIX1 1 -0.996310 -0.033870 -0.078870 71.25100 1 +MTRIX2 1 0.048050 -0.981470 -0.185470 2.71100 1 +MTRIX3 1 -0.071130 -0.188580 0.979480 2.05300 1 +ATOM 1 N GLY A 1 42.375 -12.180 24.780 1.00 35.31 N +ATOM 2 CA GLY A 1 43.603 -11.488 24.325 1.00 35.57 C +ATOM 3 C GLY A 1 43.288 -10.171 23.615 1.00 34.64 C +ATOM 4 O GLY A 1 42.111 -9.896 23.277 1.00 35.82 O +ATOM 5 N ILE A 2 44.323 -9.391 23.299 1.00 32.23 N +ATOM 6 CA ILE A 2 44.200 -8.183 22.475 1.00 27.55 C +ATOM 7 C ILE A 2 43.750 -8.629 21.119 1.00 24.92 C +ATOM 8 O ILE A 2 43.068 -7.904 20.409 1.00 23.73 O +ATOM 9 CB ILE A 2 45.525 -7.320 22.425 1.00 30.10 C +ATOM 10 CG1 ILE A 2 45.924 -6.837 23.820 1.00 29.64 C +ATOM 11 CG2 ILE A 2 45.555 -6.173 21.386 1.00 30.54 C +ATOM 12 CD1 ILE A 2 44.837 -6.338 24.762 1.00 32.44 C +ATOM 13 N GLY A 3 44.161 -9.867 20.749 1.00 22.69 N +ATOM 14 CA GLY A 3 43.999 -10.264 19.329 1.00 21.05 C +ATOM 15 C GLY A 3 42.433 -10.405 19.166 1.00 22.08 C +ATOM 16 O GLY A 3 41.912 -10.061 18.096 1.00 22.86 O +ATOM 17 N ALA A 4 41.862 -10.961 20.191 1.00 21.60 N +ATOM 18 CA ALA A 4 40.378 -11.260 20.106 1.00 21.80 C +ATOM 19 C ALA A 4 39.584 -9.950 20.087 1.00 21.67 C +ATOM 20 O ALA A 4 38.676 -9.747 19.278 1.00 22.21 O +ATOM 21 CB ALA A 4 40.061 -12.080 21.350 1.00 22.97 C +ATOM 22 N VAL A 5 39.936 -9.001 20.956 1.00 22.13 N +ATOM 23 CA VAL A 5 39.355 -7.658 21.083 1.00 19.34 C +ATOM 24 C VAL A 5 39.536 -6.896 19.795 1.00 18.81 C +ATOM 25 O VAL A 5 38.626 -6.314 19.126 1.00 17.22 O +ATOM 26 CB VAL A 5 39.843 -6.933 22.338 1.00 20.40 C +ATOM 27 CG1 VAL A 5 39.237 -5.519 22.413 1.00 23.06 C +ATOM 28 CG2 VAL A 5 39.745 -7.587 23.653 1.00 21.67 C +ATOM 29 N LEU A 6 40.752 -7.021 19.222 1.00 16.05 N +ATOM 30 CA LEU A 6 41.062 -6.432 17.957 1.00 17.59 C +ATOM 31 C LEU A 6 40.230 -6.935 16.870 1.00 20.01 C +ATOM 32 O LEU A 6 39.649 -6.121 16.029 1.00 21.90 O +ATOM 33 CB LEU A 6 42.627 -6.461 17.880 1.00 24.58 C +ATOM 34 CG LEU A 6 43.125 -6.023 16.524 1.00 23.91 C +ATOM 35 CD1 LEU A 6 42.706 -4.584 16.210 1.00 27.44 C +ATOM 36 CD2 LEU A 6 44.669 -6.152 16.638 1.00 29.31 C +ATOM 37 N LYS A 7 39.981 -8.229 16.721 1.00 19.83 N +ATOM 38 CA LYS A 7 39.079 -8.646 15.636 1.00 22.55 C +ATOM 39 C LYS A 7 37.648 -8.063 15.784 1.00 19.04 C +ATOM 40 O LYS A 7 37.031 -7.839 14.731 1.00 21.18 O +ATOM 41 CB LYS A 7 38.854 -10.176 15.616 1.00 27.62 C +ATOM 42 CG LYS A 7 40.011 -10.993 15.144 1.00 40.15 C +ATOM 43 CD LYS A 7 39.691 -12.487 15.325 1.00 47.84 C +ATOM 44 CE LYS A 7 40.599 -13.394 14.493 1.00 53.11 C +ATOM 45 NZ LYS A 7 39.966 -14.755 14.319 1.00 55.47 N +ATOM 46 N VAL A 8 37.111 -7.988 16.981 1.00 19.69 N +ATOM 47 CA VAL A 8 35.792 -7.369 17.211 1.00 20.52 C +ATOM 48 C VAL A 8 35.776 -5.881 16.885 1.00 20.31 C +ATOM 49 O VAL A 8 34.775 -5.402 16.257 1.00 20.12 O +ATOM 50 CB VAL A 8 35.113 -7.600 18.562 1.00 23.09 C +ATOM 51 CG1 VAL A 8 34.774 -9.045 18.851 1.00 24.22 C +ATOM 52 CG2 VAL A 8 35.769 -6.970 19.726 1.00 27.95 C +ATOM 53 N LEU A 9 36.860 -5.176 17.216 1.00 19.55 N +ATOM 54 CA LEU A 9 36.899 -3.759 16.725 1.00 16.83 C +ATOM 55 C LEU A 9 36.778 -3.644 15.254 1.00 19.11 C +ATOM 56 O LEU A 9 36.328 -2.551 14.694 1.00 19.69 O +ATOM 57 CB LEU A 9 38.227 -3.088 17.147 1.00 16.57 C +ATOM 58 CG LEU A 9 38.462 -3.091 18.615 1.00 18.69 C +ATOM 59 CD1 LEU A 9 39.783 -2.288 18.873 1.00 24.09 C +ATOM 60 CD2 LEU A 9 37.265 -2.535 19.351 1.00 22.17 C +ATOM 61 N THR A 10 37.320 -4.627 14.530 1.00 19.39 N +ATOM 62 CA THR A 10 37.338 -4.508 13.084 1.00 19.41 C +ATOM 63 C THR A 10 36.072 -5.022 12.458 1.00 21.08 C +ATOM 64 O THR A 10 35.694 -4.554 11.333 1.00 21.48 O +ATOM 65 CB THR A 10 38.687 -5.179 12.486 1.00 24.07 C +ATOM 66 OG1 THR A 10 38.285 -6.538 12.354 1.00 31.20 O +ATOM 67 CG2 THR A 10 39.877 -5.049 13.451 1.00 20.75 C +ATOM 68 N THR A 11 35.315 -5.870 13.113 1.00 21.12 N +ATOM 69 CA THR A 11 34.132 -6.405 12.343 1.00 24.14 C +ATOM 70 C THR A 11 32.874 -6.299 13.140 1.00 24.13 C +ATOM 71 O THR A 11 31.823 -5.889 12.630 1.00 27.78 O +ATOM 72 CB THR A 11 34.462 -7.925 11.935 1.00 27.78 C +ATOM 73 OG1 THR A 11 34.702 -8.591 13.199 1.00 31.22 O +ATOM 74 CG2 THR A 11 35.695 -7.959 11.047 1.00 30.31 C +ATOM 75 N GLY A 12 32.918 -6.606 14.420 1.00 23.00 N +ATOM 76 CA GLY A 12 31.584 -6.595 15.140 1.00 24.17 C +ATOM 77 C GLY A 12 31.264 -5.168 15.584 1.00 24.45 C +ATOM 78 O GLY A 12 30.060 -4.914 15.603 1.00 23.79 O +ATOM 79 N LEU A 13 32.195 -4.276 15.948 1.00 22.05 N +ATOM 80 CA LEU A 13 31.923 -2.919 16.364 1.00 23.24 C +ATOM 81 C LEU A 13 31.251 -2.004 15.324 1.00 21.24 C +ATOM 82 O LEU A 13 30.232 -1.308 15.679 1.00 23.02 O +ATOM 83 CB LEU A 13 33.146 -2.183 17.008 1.00 25.55 C +ATOM 84 CG LEU A 13 32.913 -1.523 18.351 1.00 27.01 C +ATOM 85 CD1 LEU A 13 33.999 -0.517 18.760 1.00 27.53 C +ATOM 86 CD2 LEU A 13 31.587 -0.842 18.531 1.00 24.54 C +ATOM 87 N PRO A 14 31.689 -1.979 14.106 1.00 17.38 N +ATOM 88 CA PRO A 14 31.026 -1.278 13.030 1.00 17.52 C +ATOM 89 C PRO A 14 29.521 -1.670 12.857 1.00 18.98 C +ATOM 90 O PRO A 14 28.657 -0.801 12.744 1.00 16.75 O +ATOM 91 CB PRO A 14 31.845 -1.614 11.816 1.00 17.80 C +ATOM 92 CG PRO A 14 33.118 -2.205 12.303 1.00 18.05 C +ATOM 93 CD PRO A 14 33.098 -2.363 13.769 1.00 17.96 C +END diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/2mlt_frag1.seq b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/2mlt_frag1.seq new file mode 100644 index 00000000..005694d8 --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/2mlt_frag1.seq @@ -0,0 +1 @@ +GIGAVLKVLTTGLP diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/2mlt_frag1/2mlt_frag1-cleaned.pdb b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/2mlt_frag1/2mlt_frag1-cleaned.pdb new file mode 100644 index 00000000..4f7baad3 --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/2mlt_frag1/2mlt_frag1-cleaned.pdb @@ -0,0 +1,210 @@ +REMARK 1 CREATED WITH OPENMM 8.1.1, 2025-12-23 +CRYST1 60.832 38.293 42.211 90.00 90.00 90.00 P 1 1 +ATOM 1 N GLY A 1 42.375 -12.180 24.780 1.00 0.00 N +ATOM 2 H GLY A 1 41.348 -11.623 25.042 1.00 0.00 H +ATOM 3 H2 GLY A 1 42.555 -12.690 25.854 1.00 0.00 H +ATOM 4 H3 GLY A 1 42.134 -13.162 24.137 1.00 0.00 H +ATOM 5 CA GLY A 1 43.603 -11.488 24.325 1.00 0.00 C +ATOM 6 HA2 GLY A 1 44.221 -11.213 25.312 1.00 0.00 H +ATOM 7 HA3 GLY A 1 44.301 -12.238 23.709 1.00 0.00 H +ATOM 8 C GLY A 1 43.288 -10.171 23.615 1.00 0.00 C +ATOM 9 O GLY A 1 42.111 -9.896 23.277 1.00 0.00 O +ATOM 10 N ILE A 2 44.323 -9.391 23.299 1.00 0.00 N +ATOM 11 H ILE A 2 45.380 -9.782 23.682 1.00 0.00 H +ATOM 12 CA ILE A 2 44.200 -8.183 22.475 1.00 0.00 C +ATOM 13 HA ILE A 2 43.338 -7.478 22.886 1.00 0.00 H +ATOM 14 C ILE A 2 43.750 -8.629 21.119 1.00 0.00 C +ATOM 15 O ILE A 2 43.068 -7.904 20.409 1.00 0.00 O +ATOM 16 CB ILE A 2 45.525 -7.320 22.425 1.00 0.00 C +ATOM 17 HB ILE A 2 46.450 -7.997 22.088 1.00 0.00 H +ATOM 18 CG1 ILE A 2 45.924 -6.837 23.820 1.00 0.00 C +ATOM 19 HG12 ILE A 2 46.792 -6.010 23.800 1.00 0.00 H +ATOM 20 HG13 ILE A 2 46.531 -7.674 24.425 1.00 0.00 H +ATOM 21 CG2 ILE A 2 45.555 -6.173 21.386 1.00 0.00 C +ATOM 22 HG21 ILE A 2 44.588 -5.494 21.214 1.00 0.00 H +ATOM 23 HG22 ILE A 2 46.339 -5.297 21.634 1.00 0.00 H +ATOM 24 HG23 ILE A 2 46.069 -6.532 20.365 1.00 0.00 H +ATOM 25 CD1 ILE A 2 44.837 -6.338 24.762 1.00 0.00 C +ATOM 26 HD11 ILE A 2 45.139 -5.222 25.094 1.00 0.00 H +ATOM 27 HD12 ILE A 2 44.872 -6.908 25.818 1.00 0.00 H +ATOM 28 HD13 ILE A 2 43.661 -6.128 24.665 1.00 0.00 H +ATOM 29 N GLY A 3 44.161 -9.867 20.749 1.00 0.00 N +ATOM 30 H GLY A 3 45.133 -10.465 21.085 1.00 0.00 H +ATOM 31 CA GLY A 3 43.999 -10.264 19.329 1.00 0.00 C +ATOM 32 HA2 GLY A 3 44.702 -9.646 18.587 1.00 0.00 H +ATOM 33 HA3 GLY A 3 44.390 -11.358 19.035 1.00 0.00 H +ATOM 34 C GLY A 3 42.433 -10.405 19.166 1.00 0.00 C +ATOM 35 O GLY A 3 41.912 -10.061 18.096 1.00 0.00 O +ATOM 36 N ALA A 4 41.862 -10.961 20.191 1.00 0.00 N +ATOM 37 H ALA A 4 42.465 -11.922 20.552 1.00 0.00 H +ATOM 38 CA ALA A 4 40.378 -11.260 20.106 1.00 0.00 C +ATOM 39 HA ALA A 4 40.148 -11.961 19.170 1.00 0.00 H +ATOM 40 C ALA A 4 39.584 -9.950 20.087 1.00 0.00 C +ATOM 41 O ALA A 4 38.676 -9.747 19.278 1.00 0.00 O +ATOM 42 CB ALA A 4 40.061 -12.080 21.350 1.00 0.00 C +ATOM 43 HB1 ALA A 4 39.843 -11.708 22.467 1.00 0.00 H +ATOM 44 HB2 ALA A 4 40.636 -13.124 21.485 1.00 0.00 H +ATOM 45 HB3 ALA A 4 38.960 -12.518 21.142 1.00 0.00 H +ATOM 46 N VAL A 5 39.936 -9.001 20.956 1.00 0.00 N +ATOM 47 H VAL A 5 40.629 -9.354 21.844 1.00 0.00 H +ATOM 48 CA VAL A 5 39.355 -7.658 21.083 1.00 0.00 C +ATOM 49 HA VAL A 5 38.259 -7.965 21.431 1.00 0.00 H +ATOM 50 C VAL A 5 39.536 -6.896 19.795 1.00 0.00 C +ATOM 51 O VAL A 5 38.626 -6.314 19.126 1.00 0.00 O +ATOM 52 CB VAL A 5 39.843 -6.933 22.338 1.00 0.00 C +ATOM 53 HB VAL A 5 40.988 -6.605 22.371 1.00 0.00 H +ATOM 54 CG1 VAL A 5 39.237 -5.519 22.413 1.00 0.00 C +ATOM 55 HG11 VAL A 5 38.051 -5.502 22.584 1.00 0.00 H +ATOM 56 HG12 VAL A 5 39.563 -4.681 21.625 1.00 0.00 H +ATOM 57 HG13 VAL A 5 39.559 -4.865 23.372 1.00 0.00 H +ATOM 58 CG2 VAL A 5 39.745 -7.587 23.653 1.00 0.00 C +ATOM 59 HG21 VAL A 5 39.713 -6.840 24.597 1.00 0.00 H +ATOM 60 HG22 VAL A 5 38.700 -8.144 23.855 1.00 0.00 H +ATOM 61 HG23 VAL A 5 40.504 -8.343 24.190 1.00 0.00 H +ATOM 62 N LEU A 6 40.752 -7.021 19.222 1.00 0.00 N +ATOM 63 H LEU A 6 41.432 -6.456 20.018 1.00 0.00 H +ATOM 64 CA LEU A 6 41.062 -6.432 17.957 1.00 0.00 C +ATOM 65 HA LEU A 6 40.866 -5.262 18.044 1.00 0.00 H +ATOM 66 C LEU A 6 40.230 -6.935 16.870 1.00 0.00 C +ATOM 67 O LEU A 6 39.649 -6.121 16.029 1.00 0.00 O +ATOM 68 CB LEU A 6 42.627 -6.461 17.880 1.00 0.00 C +ATOM 69 HB2 LEU A 6 43.172 -5.759 18.678 1.00 0.00 H +ATOM 70 HB3 LEU A 6 42.971 -7.600 17.910 1.00 0.00 H +ATOM 71 CG LEU A 6 43.125 -6.023 16.524 1.00 0.00 C +ATOM 72 HG LEU A 6 42.903 -6.713 15.576 1.00 0.00 H +ATOM 73 CD1 LEU A 6 42.706 -4.584 16.210 1.00 0.00 C +ATOM 74 HD11 LEU A 6 43.272 -4.298 15.188 1.00 0.00 H +ATOM 75 HD12 LEU A 6 43.196 -3.769 16.945 1.00 0.00 H +ATOM 76 HD13 LEU A 6 41.687 -4.015 15.951 1.00 0.00 H +ATOM 77 CD2 LEU A 6 44.669 -6.152 16.638 1.00 0.00 C +ATOM 78 HD21 LEU A 6 45.189 -5.937 15.574 1.00 0.00 H +ATOM 79 HD22 LEU A 6 45.323 -5.404 17.311 1.00 0.00 H +ATOM 80 HD23 LEU A 6 45.194 -7.216 16.816 1.00 0.00 H +ATOM 81 N LYS A 7 39.981 -8.229 16.721 1.00 0.00 N +ATOM 82 H LYS A 7 40.772 -9.075 16.935 1.00 0.00 H +ATOM 83 CA LYS A 7 39.079 -8.646 15.636 1.00 0.00 C +ATOM 84 HA LYS A 7 39.583 -8.378 14.590 1.00 0.00 H +ATOM 85 C LYS A 7 37.648 -8.063 15.784 1.00 0.00 C +ATOM 86 O LYS A 7 37.031 -7.839 14.731 1.00 0.00 O +ATOM 87 CB LYS A 7 38.854 -10.176 15.616 1.00 0.00 C +ATOM 88 HB2 LYS A 7 37.977 -10.374 14.825 1.00 0.00 H +ATOM 89 HB3 LYS A 7 38.398 -10.663 16.606 1.00 0.00 H +ATOM 90 CG LYS A 7 40.011 -10.993 15.144 1.00 0.00 C +ATOM 91 HG2 LYS A 7 41.158 -10.886 15.464 1.00 0.00 H +ATOM 92 HG3 LYS A 7 40.110 -10.782 13.968 1.00 0.00 H +ATOM 93 CD LYS A 7 39.691 -12.487 15.325 1.00 0.00 C +ATOM 94 HD2 LYS A 7 39.801 -12.898 16.441 1.00 0.00 H +ATOM 95 HD3 LYS A 7 38.586 -12.748 14.951 1.00 0.00 H +ATOM 96 CE LYS A 7 40.599 -13.394 14.493 1.00 0.00 C +ATOM 97 HE2 LYS A 7 41.676 -13.535 14.991 1.00 0.00 H +ATOM 98 HE3 LYS A 7 40.872 -13.049 13.380 1.00 0.00 H +ATOM 99 NZ LYS A 7 39.966 -14.755 14.319 1.00 0.00 N +ATOM 100 HZ1 LYS A 7 39.465 -14.898 13.239 1.00 0.00 H +ATOM 101 HZ2 LYS A 7 40.794 -15.623 14.363 1.00 0.00 H +ATOM 102 HZ3 LYS A 7 39.153 -15.222 15.066 1.00 0.00 H +ATOM 103 N VAL A 8 37.111 -7.988 16.981 1.00 0.00 N +ATOM 104 H VAL A 8 37.403 -8.767 17.821 1.00 0.00 H +ATOM 105 CA VAL A 8 35.792 -7.369 17.211 1.00 0.00 C +ATOM 106 HA VAL A 8 35.091 -8.010 16.491 1.00 0.00 H +ATOM 107 C VAL A 8 35.776 -5.881 16.885 1.00 0.00 C +ATOM 108 O VAL A 8 34.775 -5.402 16.257 1.00 0.00 O +ATOM 109 CB VAL A 8 35.113 -7.600 18.562 1.00 0.00 C +ATOM 110 HB VAL A 8 34.034 -7.086 18.529 1.00 0.00 H +ATOM 111 CG1 VAL A 8 34.774 -9.045 18.851 1.00 0.00 C +ATOM 112 HG11 VAL A 8 33.742 -9.377 18.329 1.00 0.00 H +ATOM 113 HG12 VAL A 8 34.457 -9.332 19.975 1.00 0.00 H +ATOM 114 HG13 VAL A 8 35.415 -10.026 18.593 1.00 0.00 H +ATOM 115 CG2 VAL A 8 35.769 -6.970 19.726 1.00 0.00 C +ATOM 116 HG21 VAL A 8 36.472 -7.757 20.279 1.00 0.00 H +ATOM 117 HG22 VAL A 8 36.066 -5.819 19.842 1.00 0.00 H +ATOM 118 HG23 VAL A 8 34.929 -6.899 20.590 1.00 0.00 H +ATOM 119 N LEU A 9 36.860 -5.176 17.216 1.00 0.00 N +ATOM 120 H LEU A 9 37.858 -5.414 17.783 1.00 0.00 H +ATOM 121 CA LEU A 9 36.899 -3.759 16.725 1.00 0.00 C +ATOM 122 HA LEU A 9 36.033 -3.017 17.052 1.00 0.00 H +ATOM 123 C LEU A 9 36.778 -3.644 15.254 1.00 0.00 C +ATOM 124 O LEU A 9 36.328 -2.551 14.694 1.00 0.00 O +ATOM 125 CB LEU A 9 38.227 -3.088 17.147 1.00 0.00 C +ATOM 126 HB2 LEU A 9 39.189 -3.378 16.504 1.00 0.00 H +ATOM 127 HB3 LEU A 9 38.137 -1.956 16.758 1.00 0.00 H +ATOM 128 CG LEU A 9 38.462 -3.091 18.615 1.00 0.00 C +ATOM 129 HG LEU A 9 38.754 -3.955 19.375 1.00 0.00 H +ATOM 130 CD1 LEU A 9 39.783 -2.288 18.873 1.00 0.00 C +ATOM 131 HD11 LEU A 9 40.856 -2.781 19.080 1.00 0.00 H +ATOM 132 HD12 LEU A 9 39.745 -1.582 19.847 1.00 0.00 H +ATOM 133 HD13 LEU A 9 40.098 -1.424 18.099 1.00 0.00 H +ATOM 134 CD2 LEU A 9 37.265 -2.535 19.351 1.00 0.00 C +ATOM 135 HD21 LEU A 9 37.115 -1.380 19.067 1.00 0.00 H +ATOM 136 HD22 LEU A 9 36.218 -3.088 19.520 1.00 0.00 H +ATOM 137 HD23 LEU A 9 37.478 -2.347 20.522 1.00 0.00 H +ATOM 138 N THR A 10 37.320 -4.627 14.530 1.00 0.00 N +ATOM 139 H THR A 10 37.840 -5.625 14.880 1.00 0.00 H +ATOM 140 CA THR A 10 37.338 -4.508 13.084 1.00 0.00 C +ATOM 141 HA THR A 10 37.440 -3.390 12.679 1.00 0.00 H +ATOM 142 C THR A 10 36.072 -5.022 12.458 1.00 0.00 C +ATOM 143 O THR A 10 35.694 -4.554 11.333 1.00 0.00 O +ATOM 144 CB THR A 10 38.687 -5.179 12.486 1.00 0.00 C +ATOM 145 HB THR A 10 38.867 -4.707 11.403 1.00 0.00 H +ATOM 146 OG1 THR A 10 38.285 -6.538 12.354 1.00 0.00 O +ATOM 147 HG1 THR A 10 39.022 -7.085 11.599 1.00 0.00 H +ATOM 148 CG2 THR A 10 39.877 -5.049 13.451 1.00 0.00 C +ATOM 149 HG21 THR A 10 40.525 -5.741 14.176 1.00 0.00 H +ATOM 150 HG22 THR A 10 40.717 -5.188 12.594 1.00 0.00 H +ATOM 151 HG23 THR A 10 40.027 -3.875 13.642 1.00 0.00 H +ATOM 152 N THR A 11 35.315 -5.870 13.113 1.00 0.00 N +ATOM 153 H THR A 11 35.402 -6.359 14.181 1.00 0.00 H +ATOM 154 CA THR A 11 34.132 -6.405 12.343 1.00 0.00 C +ATOM 155 HA THR A 11 33.776 -5.952 11.299 1.00 0.00 H +ATOM 156 C THR A 11 32.874 -6.299 13.140 1.00 0.00 C +ATOM 157 O THR A 11 31.823 -5.889 12.630 1.00 0.00 O +ATOM 158 CB THR A 11 34.462 -7.925 11.935 1.00 0.00 C +ATOM 159 HB THR A 11 33.509 -8.482 11.478 1.00 0.00 H +ATOM 160 OG1 THR A 11 34.702 -8.591 13.199 1.00 0.00 O +ATOM 161 HG1 THR A 11 34.748 -9.764 13.020 1.00 0.00 H +ATOM 162 CG2 THR A 11 35.695 -7.959 11.047 1.00 0.00 C +ATOM 163 HG21 THR A 11 35.174 -7.957 9.962 1.00 0.00 H +ATOM 164 HG22 THR A 11 36.601 -7.258 10.698 1.00 0.00 H +ATOM 165 HG23 THR A 11 36.212 -9.042 11.053 1.00 0.00 H +ATOM 166 N GLY A 12 32.918 -6.606 14.420 1.00 0.00 N +ATOM 167 H GLY A 12 33.201 -7.715 14.741 1.00 0.00 H +ATOM 168 CA GLY A 12 31.584 -6.595 15.140 1.00 0.00 C +ATOM 169 HA2 GLY A 12 31.429 -7.241 16.136 1.00 0.00 H +ATOM 170 HA3 GLY A 12 30.674 -7.036 14.498 1.00 0.00 H +ATOM 171 C GLY A 12 31.264 -5.168 15.584 1.00 0.00 C +ATOM 172 O GLY A 12 30.060 -4.914 15.603 1.00 0.00 O +ATOM 173 N LEU A 13 32.195 -4.276 15.948 1.00 0.00 N +ATOM 174 H LEU A 13 32.473 -4.884 16.934 1.00 0.00 H +ATOM 175 CA LEU A 13 31.923 -2.919 16.364 1.00 0.00 C +ATOM 176 HA LEU A 13 30.998 -3.094 17.098 1.00 0.00 H +ATOM 177 C LEU A 13 31.251 -2.004 15.324 1.00 0.00 C +ATOM 178 O LEU A 13 30.232 -1.308 15.679 1.00 0.00 O +ATOM 179 CB LEU A 13 33.146 -2.183 17.008 1.00 0.00 C +ATOM 180 HB2 LEU A 13 33.863 -3.073 17.325 1.00 0.00 H +ATOM 181 HB3 LEU A 13 33.501 -1.235 16.375 1.00 0.00 H +ATOM 182 CG LEU A 13 32.913 -1.523 18.351 1.00 0.00 C +ATOM 183 HG LEU A 13 32.879 -2.314 19.248 1.00 0.00 H +ATOM 184 CD1 LEU A 13 33.999 -0.517 18.760 1.00 0.00 C +ATOM 185 HD11 LEU A 13 34.965 -0.295 18.088 1.00 0.00 H +ATOM 186 HD12 LEU A 13 33.658 0.633 18.847 1.00 0.00 H +ATOM 187 HD13 LEU A 13 34.370 -0.681 19.889 1.00 0.00 H +ATOM 188 CD2 LEU A 13 31.587 -0.842 18.531 1.00 0.00 C +ATOM 189 HD21 LEU A 13 31.499 -0.196 19.543 1.00 0.00 H +ATOM 190 HD22 LEU A 13 31.256 0.004 17.748 1.00 0.00 H +ATOM 191 HD23 LEU A 13 30.609 -1.496 18.772 1.00 0.00 H +ATOM 192 N PRO A 14 31.689 -1.979 14.106 1.00 0.00 N +ATOM 193 CA PRO A 14 31.026 -1.278 13.030 1.00 0.00 C +ATOM 194 HA PRO A 14 30.971 -0.101 13.220 1.00 0.00 H +ATOM 195 C PRO A 14 29.521 -1.670 12.857 1.00 0.00 C +ATOM 196 O PRO A 14 28.657 -0.801 12.744 1.00 0.00 O +ATOM 197 CB PRO A 14 31.845 -1.614 11.816 1.00 0.00 C +ATOM 198 HB2 PRO A 14 31.257 -2.227 10.972 1.00 0.00 H +ATOM 199 HB3 PRO A 14 32.036 -0.613 11.183 1.00 0.00 H +ATOM 200 CG PRO A 14 33.118 -2.205 12.303 1.00 0.00 C +ATOM 201 HG2 PRO A 14 33.250 -3.166 11.606 1.00 0.00 H +ATOM 202 HG3 PRO A 14 34.010 -1.511 11.899 1.00 0.00 H +ATOM 203 CD PRO A 14 33.098 -2.363 13.769 1.00 0.00 C +ATOM 204 HD2 PRO A 14 33.564 -3.425 14.021 1.00 0.00 H +ATOM 205 HD3 PRO A 14 33.775 -1.449 14.137 1.00 0.00 H +ATOM 206 OXT PRO A 14 29.767 -2.895 12.875 1.00 0.00 O +TER 207 PRO A 14 +END diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/2mlt_frag1/2mlt_frag1-openmmawsem.pdb b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/2mlt_frag1/2mlt_frag1-openmmawsem.pdb new file mode 100644 index 00000000..8e33286a --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/2mlt_frag1/2mlt_frag1-openmmawsem.pdb @@ -0,0 +1,79 @@ +ATOM 1 CA IGL A 1 43.603 -11.488 24.325 1.00 0.00 C +ATOM 2 C IGL A 1 43.264 -10.199 23.553 1.00 0.00 C +ATOM 3 O IGL A 1 42.111 -9.896 23.277 1.00 0.00 O +ATOM 4 N NGP A 2 44.302 -9.461 23.220 1.00 0.00 N +ATOM 5 H NGP A 2 45.234 -9.706 23.444 1.00 0.00 H +ATOM 6 CA NGP A 2 44.200 -8.183 22.475 1.00 0.00 C +ATOM 7 C NGP A 2 43.789 -8.583 21.072 1.00 0.00 C +ATOM 8 O NGP A 2 43.068 -7.904 20.409 1.00 0.00 O +ATOM 9 CB NGP A 2 45.525 -7.320 22.425 1.00 0.00 B +ATOM 10 N IGL A 3 44.271 -9.699 20.648 1.00 0.00 N +ATOM 11 H IGL A 3 44.854 -10.247 21.184 1.00 0.00 H +ATOM 12 CA IGL A 3 43.999 -10.264 19.329 1.00 0.00 C +ATOM 13 C IGL A 3 42.477 -10.433 19.116 1.00 0.00 C +ATOM 14 O IGL A 3 41.912 -10.061 18.096 1.00 0.00 O +ATOM 15 N NGP A 4 41.843 -11.003 20.106 1.00 0.00 N +ATOM 16 H NGP A 4 42.300 -11.303 20.929 1.00 0.00 H +ATOM 17 CA NGP A 4 40.378 -11.260 20.106 1.00 0.00 C +ATOM 18 C NGP A 4 39.591 -9.927 20.070 1.00 0.00 C +ATOM 19 O NGP A 4 38.676 -9.747 19.278 1.00 0.00 O +ATOM 20 CB NGP A 4 40.061 -12.080 21.350 1.00 0.00 B +ATOM 21 N NGP A 5 39.977 -9.009 20.948 1.00 0.00 N +ATOM 22 H NGP A 5 40.716 -9.155 21.587 1.00 0.00 H +ATOM 23 CA NGP A 5 39.355 -7.658 21.083 1.00 0.00 C +ATOM 24 C NGP A 5 39.522 -6.938 19.719 1.00 0.00 C +ATOM 25 O NGP A 5 38.626 -6.314 19.126 1.00 0.00 O +ATOM 26 CB NGP A 5 39.843 -6.933 22.338 1.00 0.00 B +ATOM 27 N NGP A 6 40.693 -7.047 19.250 1.00 0.00 N +ATOM 28 H NGP A 6 41.417 -7.550 19.729 1.00 0.00 H +ATOM 29 CA NGP A 6 41.062 -6.432 17.957 1.00 0.00 C +ATOM 30 C NGP A 6 40.142 -6.853 16.792 1.00 0.00 C +ATOM 31 O NGP A 6 39.649 -6.121 16.029 1.00 0.00 O +ATOM 32 CB NGP A 6 42.627 -6.461 17.880 1.00 0.00 B +ATOM 33 N NGP A 7 39.932 -8.047 16.685 1.00 0.00 N +ATOM 34 H NGP A 7 40.331 -8.638 17.301 1.00 0.00 H +ATOM 35 CA NGP A 7 39.079 -8.646 15.636 1.00 0.00 C +ATOM 36 C NGP A 7 37.648 -8.086 15.716 1.00 0.00 C +ATOM 37 O NGP A 7 37.031 -7.839 14.731 1.00 0.00 O +ATOM 38 CB NGP A 7 38.854 -10.176 15.616 1.00 0.00 B +ATOM 39 N NGP A 8 37.150 -7.899 16.913 1.00 0.00 N +ATOM 40 H NGP A 8 37.650 -8.099 17.708 1.00 0.00 H +ATOM 41 CA NGP A 8 35.792 -7.369 17.211 1.00 0.00 C +ATOM 42 C NGP A 8 35.726 -5.888 16.790 1.00 0.00 C +ATOM 43 O NGP A 8 34.775 -5.402 16.257 1.00 0.00 O +ATOM 44 CB NGP A 8 35.113 -7.600 18.562 1.00 0.00 B +ATOM 45 N NGP A 9 36.761 -5.197 17.048 1.00 0.00 N +ATOM 46 H NGP A 9 37.529 -5.589 17.478 1.00 0.00 H +ATOM 47 CA NGP A 9 36.899 -3.759 16.725 1.00 0.00 C +ATOM 48 C NGP A 9 36.819 -3.547 15.216 1.00 0.00 C +ATOM 49 O NGP A 9 36.328 -2.551 14.694 1.00 0.00 O +ATOM 50 CB NGP A 9 38.227 -3.088 17.147 1.00 0.00 B +ATOM 51 N NGP A 10 37.315 -4.511 14.543 1.00 0.00 N +ATOM 52 H NGP A 10 37.713 -5.315 14.965 1.00 0.00 H +ATOM 53 CA NGP A 10 37.338 -4.508 13.084 1.00 0.00 C +ATOM 54 C NGP A 10 36.056 -4.969 12.347 1.00 0.00 C +ATOM 55 O NGP A 10 35.694 -4.554 11.333 1.00 0.00 O +ATOM 56 CB NGP A 10 38.687 -5.179 12.486 1.00 0.00 B +ATOM 57 N NGP A 11 35.391 -5.834 12.890 1.00 0.00 N +ATOM 58 H NGP A 11 35.684 -6.169 13.708 1.00 0.00 H +ATOM 59 CA NGP A 11 34.132 -6.405 12.343 1.00 0.00 C +ATOM 60 C NGP A 11 32.791 -6.284 13.093 1.00 0.00 C +ATOM 61 O NGP A 11 31.823 -5.889 12.630 1.00 0.00 O +ATOM 62 CB NGP A 11 34.462 -7.925 11.935 1.00 0.00 B +ATOM 63 N IGL A 12 32.772 -6.635 14.257 1.00 0.00 N +ATOM 64 H IGL A 12 33.554 -6.954 14.631 1.00 0.00 H +ATOM 65 CA IGL A 12 31.584 -6.595 15.140 1.00 0.00 C +ATOM 66 C IGL A 12 31.174 -5.191 15.577 1.00 0.00 C +ATOM 67 O IGL A 12 30.060 -4.914 15.603 1.00 0.00 O +ATOM 68 N NGP A 13 32.107 -4.323 15.915 1.00 0.00 N +ATOM 69 H NGP A 13 33.007 -4.547 15.894 1.00 0.00 H +ATOM 70 CA NGP A 13 31.923 -2.919 16.364 1.00 0.00 C +ATOM 71 C NGP A 13 31.169 -2.016 15.360 1.00 0.00 C +ATOM 72 O NGP A 13 30.232 -1.308 15.679 1.00 0.00 O +ATOM 73 CB NGP A 13 33.146 -2.183 17.008 1.00 0.00 B +ATOM 74 N IPR A 14 31.608 -2.065 14.147 1.00 0.00 N +ATOM 75 CA IPR A 14 31.026 -1.278 13.030 1.00 0.00 C +ATOM 76 O IPR A 14 28.657 -0.801 12.744 1.00 0.00 O +ATOM 77 CB IPR A 14 31.845 -1.614 11.816 1.00 0.00 B +TER 78 CB IPR A 14 +END diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/2mlt_frag1/2mlt_frag1.fasta b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/2mlt_frag1/2mlt_frag1.fasta new file mode 100644 index 00000000..32c6f937 --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/2mlt_frag1/2mlt_frag1.fasta @@ -0,0 +1,2 @@ +>CRYSTAL_STRUCTURE:A +GIGAVLKVLTTGLP diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/2mlt_frag1/2mlt_frag1.pdb b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/2mlt_frag1/2mlt_frag1.pdb new file mode 100644 index 00000000..4f7baad3 --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/2mlt_frag1/2mlt_frag1.pdb @@ -0,0 +1,210 @@ +REMARK 1 CREATED WITH OPENMM 8.1.1, 2025-12-23 +CRYST1 60.832 38.293 42.211 90.00 90.00 90.00 P 1 1 +ATOM 1 N GLY A 1 42.375 -12.180 24.780 1.00 0.00 N +ATOM 2 H GLY A 1 41.348 -11.623 25.042 1.00 0.00 H +ATOM 3 H2 GLY A 1 42.555 -12.690 25.854 1.00 0.00 H +ATOM 4 H3 GLY A 1 42.134 -13.162 24.137 1.00 0.00 H +ATOM 5 CA GLY A 1 43.603 -11.488 24.325 1.00 0.00 C +ATOM 6 HA2 GLY A 1 44.221 -11.213 25.312 1.00 0.00 H +ATOM 7 HA3 GLY A 1 44.301 -12.238 23.709 1.00 0.00 H +ATOM 8 C GLY A 1 43.288 -10.171 23.615 1.00 0.00 C +ATOM 9 O GLY A 1 42.111 -9.896 23.277 1.00 0.00 O +ATOM 10 N ILE A 2 44.323 -9.391 23.299 1.00 0.00 N +ATOM 11 H ILE A 2 45.380 -9.782 23.682 1.00 0.00 H +ATOM 12 CA ILE A 2 44.200 -8.183 22.475 1.00 0.00 C +ATOM 13 HA ILE A 2 43.338 -7.478 22.886 1.00 0.00 H +ATOM 14 C ILE A 2 43.750 -8.629 21.119 1.00 0.00 C +ATOM 15 O ILE A 2 43.068 -7.904 20.409 1.00 0.00 O +ATOM 16 CB ILE A 2 45.525 -7.320 22.425 1.00 0.00 C +ATOM 17 HB ILE A 2 46.450 -7.997 22.088 1.00 0.00 H +ATOM 18 CG1 ILE A 2 45.924 -6.837 23.820 1.00 0.00 C +ATOM 19 HG12 ILE A 2 46.792 -6.010 23.800 1.00 0.00 H +ATOM 20 HG13 ILE A 2 46.531 -7.674 24.425 1.00 0.00 H +ATOM 21 CG2 ILE A 2 45.555 -6.173 21.386 1.00 0.00 C +ATOM 22 HG21 ILE A 2 44.588 -5.494 21.214 1.00 0.00 H +ATOM 23 HG22 ILE A 2 46.339 -5.297 21.634 1.00 0.00 H +ATOM 24 HG23 ILE A 2 46.069 -6.532 20.365 1.00 0.00 H +ATOM 25 CD1 ILE A 2 44.837 -6.338 24.762 1.00 0.00 C +ATOM 26 HD11 ILE A 2 45.139 -5.222 25.094 1.00 0.00 H +ATOM 27 HD12 ILE A 2 44.872 -6.908 25.818 1.00 0.00 H +ATOM 28 HD13 ILE A 2 43.661 -6.128 24.665 1.00 0.00 H +ATOM 29 N GLY A 3 44.161 -9.867 20.749 1.00 0.00 N +ATOM 30 H GLY A 3 45.133 -10.465 21.085 1.00 0.00 H +ATOM 31 CA GLY A 3 43.999 -10.264 19.329 1.00 0.00 C +ATOM 32 HA2 GLY A 3 44.702 -9.646 18.587 1.00 0.00 H +ATOM 33 HA3 GLY A 3 44.390 -11.358 19.035 1.00 0.00 H +ATOM 34 C GLY A 3 42.433 -10.405 19.166 1.00 0.00 C +ATOM 35 O GLY A 3 41.912 -10.061 18.096 1.00 0.00 O +ATOM 36 N ALA A 4 41.862 -10.961 20.191 1.00 0.00 N +ATOM 37 H ALA A 4 42.465 -11.922 20.552 1.00 0.00 H +ATOM 38 CA ALA A 4 40.378 -11.260 20.106 1.00 0.00 C +ATOM 39 HA ALA A 4 40.148 -11.961 19.170 1.00 0.00 H +ATOM 40 C ALA A 4 39.584 -9.950 20.087 1.00 0.00 C +ATOM 41 O ALA A 4 38.676 -9.747 19.278 1.00 0.00 O +ATOM 42 CB ALA A 4 40.061 -12.080 21.350 1.00 0.00 C +ATOM 43 HB1 ALA A 4 39.843 -11.708 22.467 1.00 0.00 H +ATOM 44 HB2 ALA A 4 40.636 -13.124 21.485 1.00 0.00 H +ATOM 45 HB3 ALA A 4 38.960 -12.518 21.142 1.00 0.00 H +ATOM 46 N VAL A 5 39.936 -9.001 20.956 1.00 0.00 N +ATOM 47 H VAL A 5 40.629 -9.354 21.844 1.00 0.00 H +ATOM 48 CA VAL A 5 39.355 -7.658 21.083 1.00 0.00 C +ATOM 49 HA VAL A 5 38.259 -7.965 21.431 1.00 0.00 H +ATOM 50 C VAL A 5 39.536 -6.896 19.795 1.00 0.00 C +ATOM 51 O VAL A 5 38.626 -6.314 19.126 1.00 0.00 O +ATOM 52 CB VAL A 5 39.843 -6.933 22.338 1.00 0.00 C +ATOM 53 HB VAL A 5 40.988 -6.605 22.371 1.00 0.00 H +ATOM 54 CG1 VAL A 5 39.237 -5.519 22.413 1.00 0.00 C +ATOM 55 HG11 VAL A 5 38.051 -5.502 22.584 1.00 0.00 H +ATOM 56 HG12 VAL A 5 39.563 -4.681 21.625 1.00 0.00 H +ATOM 57 HG13 VAL A 5 39.559 -4.865 23.372 1.00 0.00 H +ATOM 58 CG2 VAL A 5 39.745 -7.587 23.653 1.00 0.00 C +ATOM 59 HG21 VAL A 5 39.713 -6.840 24.597 1.00 0.00 H +ATOM 60 HG22 VAL A 5 38.700 -8.144 23.855 1.00 0.00 H +ATOM 61 HG23 VAL A 5 40.504 -8.343 24.190 1.00 0.00 H +ATOM 62 N LEU A 6 40.752 -7.021 19.222 1.00 0.00 N +ATOM 63 H LEU A 6 41.432 -6.456 20.018 1.00 0.00 H +ATOM 64 CA LEU A 6 41.062 -6.432 17.957 1.00 0.00 C +ATOM 65 HA LEU A 6 40.866 -5.262 18.044 1.00 0.00 H +ATOM 66 C LEU A 6 40.230 -6.935 16.870 1.00 0.00 C +ATOM 67 O LEU A 6 39.649 -6.121 16.029 1.00 0.00 O +ATOM 68 CB LEU A 6 42.627 -6.461 17.880 1.00 0.00 C +ATOM 69 HB2 LEU A 6 43.172 -5.759 18.678 1.00 0.00 H +ATOM 70 HB3 LEU A 6 42.971 -7.600 17.910 1.00 0.00 H +ATOM 71 CG LEU A 6 43.125 -6.023 16.524 1.00 0.00 C +ATOM 72 HG LEU A 6 42.903 -6.713 15.576 1.00 0.00 H +ATOM 73 CD1 LEU A 6 42.706 -4.584 16.210 1.00 0.00 C +ATOM 74 HD11 LEU A 6 43.272 -4.298 15.188 1.00 0.00 H +ATOM 75 HD12 LEU A 6 43.196 -3.769 16.945 1.00 0.00 H +ATOM 76 HD13 LEU A 6 41.687 -4.015 15.951 1.00 0.00 H +ATOM 77 CD2 LEU A 6 44.669 -6.152 16.638 1.00 0.00 C +ATOM 78 HD21 LEU A 6 45.189 -5.937 15.574 1.00 0.00 H +ATOM 79 HD22 LEU A 6 45.323 -5.404 17.311 1.00 0.00 H +ATOM 80 HD23 LEU A 6 45.194 -7.216 16.816 1.00 0.00 H +ATOM 81 N LYS A 7 39.981 -8.229 16.721 1.00 0.00 N +ATOM 82 H LYS A 7 40.772 -9.075 16.935 1.00 0.00 H +ATOM 83 CA LYS A 7 39.079 -8.646 15.636 1.00 0.00 C +ATOM 84 HA LYS A 7 39.583 -8.378 14.590 1.00 0.00 H +ATOM 85 C LYS A 7 37.648 -8.063 15.784 1.00 0.00 C +ATOM 86 O LYS A 7 37.031 -7.839 14.731 1.00 0.00 O +ATOM 87 CB LYS A 7 38.854 -10.176 15.616 1.00 0.00 C +ATOM 88 HB2 LYS A 7 37.977 -10.374 14.825 1.00 0.00 H +ATOM 89 HB3 LYS A 7 38.398 -10.663 16.606 1.00 0.00 H +ATOM 90 CG LYS A 7 40.011 -10.993 15.144 1.00 0.00 C +ATOM 91 HG2 LYS A 7 41.158 -10.886 15.464 1.00 0.00 H +ATOM 92 HG3 LYS A 7 40.110 -10.782 13.968 1.00 0.00 H +ATOM 93 CD LYS A 7 39.691 -12.487 15.325 1.00 0.00 C +ATOM 94 HD2 LYS A 7 39.801 -12.898 16.441 1.00 0.00 H +ATOM 95 HD3 LYS A 7 38.586 -12.748 14.951 1.00 0.00 H +ATOM 96 CE LYS A 7 40.599 -13.394 14.493 1.00 0.00 C +ATOM 97 HE2 LYS A 7 41.676 -13.535 14.991 1.00 0.00 H +ATOM 98 HE3 LYS A 7 40.872 -13.049 13.380 1.00 0.00 H +ATOM 99 NZ LYS A 7 39.966 -14.755 14.319 1.00 0.00 N +ATOM 100 HZ1 LYS A 7 39.465 -14.898 13.239 1.00 0.00 H +ATOM 101 HZ2 LYS A 7 40.794 -15.623 14.363 1.00 0.00 H +ATOM 102 HZ3 LYS A 7 39.153 -15.222 15.066 1.00 0.00 H +ATOM 103 N VAL A 8 37.111 -7.988 16.981 1.00 0.00 N +ATOM 104 H VAL A 8 37.403 -8.767 17.821 1.00 0.00 H +ATOM 105 CA VAL A 8 35.792 -7.369 17.211 1.00 0.00 C +ATOM 106 HA VAL A 8 35.091 -8.010 16.491 1.00 0.00 H +ATOM 107 C VAL A 8 35.776 -5.881 16.885 1.00 0.00 C +ATOM 108 O VAL A 8 34.775 -5.402 16.257 1.00 0.00 O +ATOM 109 CB VAL A 8 35.113 -7.600 18.562 1.00 0.00 C +ATOM 110 HB VAL A 8 34.034 -7.086 18.529 1.00 0.00 H +ATOM 111 CG1 VAL A 8 34.774 -9.045 18.851 1.00 0.00 C +ATOM 112 HG11 VAL A 8 33.742 -9.377 18.329 1.00 0.00 H +ATOM 113 HG12 VAL A 8 34.457 -9.332 19.975 1.00 0.00 H +ATOM 114 HG13 VAL A 8 35.415 -10.026 18.593 1.00 0.00 H +ATOM 115 CG2 VAL A 8 35.769 -6.970 19.726 1.00 0.00 C +ATOM 116 HG21 VAL A 8 36.472 -7.757 20.279 1.00 0.00 H +ATOM 117 HG22 VAL A 8 36.066 -5.819 19.842 1.00 0.00 H +ATOM 118 HG23 VAL A 8 34.929 -6.899 20.590 1.00 0.00 H +ATOM 119 N LEU A 9 36.860 -5.176 17.216 1.00 0.00 N +ATOM 120 H LEU A 9 37.858 -5.414 17.783 1.00 0.00 H +ATOM 121 CA LEU A 9 36.899 -3.759 16.725 1.00 0.00 C +ATOM 122 HA LEU A 9 36.033 -3.017 17.052 1.00 0.00 H +ATOM 123 C LEU A 9 36.778 -3.644 15.254 1.00 0.00 C +ATOM 124 O LEU A 9 36.328 -2.551 14.694 1.00 0.00 O +ATOM 125 CB LEU A 9 38.227 -3.088 17.147 1.00 0.00 C +ATOM 126 HB2 LEU A 9 39.189 -3.378 16.504 1.00 0.00 H +ATOM 127 HB3 LEU A 9 38.137 -1.956 16.758 1.00 0.00 H +ATOM 128 CG LEU A 9 38.462 -3.091 18.615 1.00 0.00 C +ATOM 129 HG LEU A 9 38.754 -3.955 19.375 1.00 0.00 H +ATOM 130 CD1 LEU A 9 39.783 -2.288 18.873 1.00 0.00 C +ATOM 131 HD11 LEU A 9 40.856 -2.781 19.080 1.00 0.00 H +ATOM 132 HD12 LEU A 9 39.745 -1.582 19.847 1.00 0.00 H +ATOM 133 HD13 LEU A 9 40.098 -1.424 18.099 1.00 0.00 H +ATOM 134 CD2 LEU A 9 37.265 -2.535 19.351 1.00 0.00 C +ATOM 135 HD21 LEU A 9 37.115 -1.380 19.067 1.00 0.00 H +ATOM 136 HD22 LEU A 9 36.218 -3.088 19.520 1.00 0.00 H +ATOM 137 HD23 LEU A 9 37.478 -2.347 20.522 1.00 0.00 H +ATOM 138 N THR A 10 37.320 -4.627 14.530 1.00 0.00 N +ATOM 139 H THR A 10 37.840 -5.625 14.880 1.00 0.00 H +ATOM 140 CA THR A 10 37.338 -4.508 13.084 1.00 0.00 C +ATOM 141 HA THR A 10 37.440 -3.390 12.679 1.00 0.00 H +ATOM 142 C THR A 10 36.072 -5.022 12.458 1.00 0.00 C +ATOM 143 O THR A 10 35.694 -4.554 11.333 1.00 0.00 O +ATOM 144 CB THR A 10 38.687 -5.179 12.486 1.00 0.00 C +ATOM 145 HB THR A 10 38.867 -4.707 11.403 1.00 0.00 H +ATOM 146 OG1 THR A 10 38.285 -6.538 12.354 1.00 0.00 O +ATOM 147 HG1 THR A 10 39.022 -7.085 11.599 1.00 0.00 H +ATOM 148 CG2 THR A 10 39.877 -5.049 13.451 1.00 0.00 C +ATOM 149 HG21 THR A 10 40.525 -5.741 14.176 1.00 0.00 H +ATOM 150 HG22 THR A 10 40.717 -5.188 12.594 1.00 0.00 H +ATOM 151 HG23 THR A 10 40.027 -3.875 13.642 1.00 0.00 H +ATOM 152 N THR A 11 35.315 -5.870 13.113 1.00 0.00 N +ATOM 153 H THR A 11 35.402 -6.359 14.181 1.00 0.00 H +ATOM 154 CA THR A 11 34.132 -6.405 12.343 1.00 0.00 C +ATOM 155 HA THR A 11 33.776 -5.952 11.299 1.00 0.00 H +ATOM 156 C THR A 11 32.874 -6.299 13.140 1.00 0.00 C +ATOM 157 O THR A 11 31.823 -5.889 12.630 1.00 0.00 O +ATOM 158 CB THR A 11 34.462 -7.925 11.935 1.00 0.00 C +ATOM 159 HB THR A 11 33.509 -8.482 11.478 1.00 0.00 H +ATOM 160 OG1 THR A 11 34.702 -8.591 13.199 1.00 0.00 O +ATOM 161 HG1 THR A 11 34.748 -9.764 13.020 1.00 0.00 H +ATOM 162 CG2 THR A 11 35.695 -7.959 11.047 1.00 0.00 C +ATOM 163 HG21 THR A 11 35.174 -7.957 9.962 1.00 0.00 H +ATOM 164 HG22 THR A 11 36.601 -7.258 10.698 1.00 0.00 H +ATOM 165 HG23 THR A 11 36.212 -9.042 11.053 1.00 0.00 H +ATOM 166 N GLY A 12 32.918 -6.606 14.420 1.00 0.00 N +ATOM 167 H GLY A 12 33.201 -7.715 14.741 1.00 0.00 H +ATOM 168 CA GLY A 12 31.584 -6.595 15.140 1.00 0.00 C +ATOM 169 HA2 GLY A 12 31.429 -7.241 16.136 1.00 0.00 H +ATOM 170 HA3 GLY A 12 30.674 -7.036 14.498 1.00 0.00 H +ATOM 171 C GLY A 12 31.264 -5.168 15.584 1.00 0.00 C +ATOM 172 O GLY A 12 30.060 -4.914 15.603 1.00 0.00 O +ATOM 173 N LEU A 13 32.195 -4.276 15.948 1.00 0.00 N +ATOM 174 H LEU A 13 32.473 -4.884 16.934 1.00 0.00 H +ATOM 175 CA LEU A 13 31.923 -2.919 16.364 1.00 0.00 C +ATOM 176 HA LEU A 13 30.998 -3.094 17.098 1.00 0.00 H +ATOM 177 C LEU A 13 31.251 -2.004 15.324 1.00 0.00 C +ATOM 178 O LEU A 13 30.232 -1.308 15.679 1.00 0.00 O +ATOM 179 CB LEU A 13 33.146 -2.183 17.008 1.00 0.00 C +ATOM 180 HB2 LEU A 13 33.863 -3.073 17.325 1.00 0.00 H +ATOM 181 HB3 LEU A 13 33.501 -1.235 16.375 1.00 0.00 H +ATOM 182 CG LEU A 13 32.913 -1.523 18.351 1.00 0.00 C +ATOM 183 HG LEU A 13 32.879 -2.314 19.248 1.00 0.00 H +ATOM 184 CD1 LEU A 13 33.999 -0.517 18.760 1.00 0.00 C +ATOM 185 HD11 LEU A 13 34.965 -0.295 18.088 1.00 0.00 H +ATOM 186 HD12 LEU A 13 33.658 0.633 18.847 1.00 0.00 H +ATOM 187 HD13 LEU A 13 34.370 -0.681 19.889 1.00 0.00 H +ATOM 188 CD2 LEU A 13 31.587 -0.842 18.531 1.00 0.00 C +ATOM 189 HD21 LEU A 13 31.499 -0.196 19.543 1.00 0.00 H +ATOM 190 HD22 LEU A 13 31.256 0.004 17.748 1.00 0.00 H +ATOM 191 HD23 LEU A 13 30.609 -1.496 18.772 1.00 0.00 H +ATOM 192 N PRO A 14 31.689 -1.979 14.106 1.00 0.00 N +ATOM 193 CA PRO A 14 31.026 -1.278 13.030 1.00 0.00 C +ATOM 194 HA PRO A 14 30.971 -0.101 13.220 1.00 0.00 H +ATOM 195 C PRO A 14 29.521 -1.670 12.857 1.00 0.00 C +ATOM 196 O PRO A 14 28.657 -0.801 12.744 1.00 0.00 O +ATOM 197 CB PRO A 14 31.845 -1.614 11.816 1.00 0.00 C +ATOM 198 HB2 PRO A 14 31.257 -2.227 10.972 1.00 0.00 H +ATOM 199 HB3 PRO A 14 32.036 -0.613 11.183 1.00 0.00 H +ATOM 200 CG PRO A 14 33.118 -2.205 12.303 1.00 0.00 C +ATOM 201 HG2 PRO A 14 33.250 -3.166 11.606 1.00 0.00 H +ATOM 202 HG3 PRO A 14 34.010 -1.511 11.899 1.00 0.00 H +ATOM 203 CD PRO A 14 33.098 -2.363 13.769 1.00 0.00 C +ATOM 204 HD2 PRO A 14 33.564 -3.425 14.021 1.00 0.00 H +ATOM 205 HD3 PRO A 14 33.775 -1.449 14.137 1.00 0.00 H +ATOM 206 OXT PRO A 14 29.767 -2.895 12.875 1.00 0.00 O +TER 207 PRO A 14 +END diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/2mlt_frag1/2mlt_frag1_A.gro b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/2mlt_frag1/2mlt_frag1_A.gro new file mode 100644 index 00000000..f998b252 --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/2mlt_frag1/2mlt_frag1_A.gro @@ -0,0 +1,208 @@ + Structure-Based gro file + 206 + 1 GLY N 1 4.238 -1.218 2.478 + 1 GLY H 2 4.135 -1.162 2.504 + 1 GLY H2 3 4.256 -1.269 2.585 + 1 GLY H3 4 4.213 -1.316 2.414 + 1 GLY CA 5 4.36 -1.149 2.433 + 1 GLY HA2 6 4.422 -1.121 2.531 + 1 GLY HA3 7 4.43 -1.224 2.371 + 1 GLY C 8 4.329 -1.017 2.361 + 1 GLY O 9 4.211 -0.99 2.328 + 2 ILE N 10 4.432 -0.939 2.33 + 2 ILE H 11 4.538 -0.978 2.368 + 2 ILE CA 12 4.42 -0.818 2.248 + 2 ILE HA 13 4.334 -0.748 2.289 + 2 ILE C 14 4.375 -0.863 2.112 + 2 ILE O 15 4.307 -0.79 2.041 + 2 ILE CB 16 4.553 -0.732 2.242 + 2 ILE HB 17 4.645 -0.8 2.209 + 2 ILE CG1 18 4.592 -0.684 2.382 + 2 ILE HG12 19 4.679 -0.601 2.38 + 2 ILE HG13 20 4.653 -0.767 2.442 + 2 ILE CG2 21 4.556 -0.617 2.139 + 2 ILE HG21 22 4.459 -0.549 2.121 + 2 ILE HG22 23 4.634 -0.53 2.163 + 2 ILE HG23 24 4.607 -0.653 2.036 + 2 ILE CD1 25 4.484 -0.634 2.476 + 2 ILE HD11 26 4.514 -0.522 2.509 + 2 ILE HD12 27 4.487 -0.691 2.582 + 2 ILE HD13 28 4.366 -0.613 2.467 + 3 GLY N 29 4.416 -0.987 2.075 + 3 GLY H 30 4.513 -1.047 2.108 + 3 GLY CA 31 4.4 -1.026 1.933 + 3 GLY HA2 32 4.47 -0.965 1.859 + 3 GLY HA3 33 4.439 -1.136 1.903 + 3 GLY C 34 4.243 -1.04 1.917 + 3 GLY O 35 4.191 -1.006 1.81 + 4 ALA N 36 4.186 -1.096 2.019 + 4 ALA H 37 4.247 -1.192 2.055 + 4 ALA CA 38 4.038 -1.126 2.011 + 4 ALA HA 39 4.015 -1.196 1.917 + 4 ALA C 40 3.958 -0.995 2.009 + 4 ALA O 41 3.868 -0.975 1.928 + 4 ALA CB 42 4.006 -1.208 2.135 + 4 ALA HB1 43 3.984 -1.171 2.247 + 4 ALA HB2 44 4.064 -1.312 2.149 + 4 ALA HB3 45 3.896 -1.252 2.114 + 5 VAL N 46 3.994 -0.9 2.096 + 5 VAL H 47 4.063 -0.935 2.184 + 5 VAL CA 48 3.935 -0.766 2.108 + 5 VAL HA 49 3.826 -0.797 2.143 + 5 VAL C 50 3.954 -0.69 1.98 + 5 VAL O 51 3.863 -0.631 1.913 + 5 VAL CB 52 3.984 -0.693 2.234 + 5 VAL HB 53 4.099 -0.661 2.237 + 5 VAL CG1 54 3.924 -0.552 2.241 + 5 VAL HG11 55 3.805 -0.55 2.258 + 5 VAL HG12 56 3.956 -0.468 2.162 + 5 VAL HG13 57 3.956 -0.486 2.337 + 5 VAL CG2 58 3.974 -0.759 2.365 + 5 VAL HG21 59 3.971 -0.684 2.46 + 5 VAL HG22 60 3.87 -0.814 2.385 + 5 VAL HG23 61 4.05 -0.834 2.419 + 6 LEU N 62 4.075 -0.702 1.922 + 6 LEU H 63 4.143 -0.646 2.002 + 6 LEU CA 64 4.106 -0.643 1.796 + 6 LEU HA 65 4.087 -0.526 1.804 + 6 LEU C 66 4.023 -0.693 1.687 + 6 LEU O 67 3.965 -0.612 1.603 + 6 LEU CB 68 4.263 -0.646 1.788 + 6 LEU HB2 69 4.317 -0.576 1.868 + 6 LEU HB3 70 4.297 -0.76 1.791 + 6 LEU CG 71 4.312 -0.602 1.652 + 6 LEU HG 72 4.29 -0.671 1.558 + 6 LEU CD1 73 4.271 -0.458 1.621 + 6 LEU HD11 74 4.327 -0.43 1.519 + 6 LEU HD12 75 4.32 -0.377 1.694 + 6 LEU HD13 76 4.169 -0.401 1.595 + 6 LEU CD2 77 4.467 -0.615 1.664 + 6 LEU HD21 78 4.519 -0.594 1.557 + 6 LEU HD22 79 4.532 -0.54 1.731 + 6 LEU HD23 80 4.519 -0.722 1.682 + 7 LYS N 81 3.998 -0.823 1.672 + 7 LYS H 82 4.077 -0.907 1.693 + 7 LYS CA 83 3.908 -0.865 1.564 + 7 LYS HA 84 3.958 -0.838 1.459 + 7 LYS C 85 3.765 -0.806 1.578 + 7 LYS O 86 3.703 -0.784 1.473 + 7 LYS CB 87 3.885 -1.018 1.562 + 7 LYS HB2 88 3.798 -1.037 1.482 + 7 LYS HB3 89 3.84 -1.066 1.661 + 7 LYS CG 90 4.001 -1.099 1.514 + 7 LYS HG2 91 4.116 -1.089 1.546 + 7 LYS HG3 92 4.011 -1.078 1.397 + 7 LYS CD 93 3.969 -1.249 1.532 + 7 LYS HD2 94 3.98 -1.29 1.644 + 7 LYS HD3 95 3.859 -1.275 1.495 + 7 LYS CE 96 4.06 -1.339 1.449 + 7 LYS HE2 97 4.168 -1.353 1.499 + 7 LYS HE3 98 4.087 -1.305 1.338 + 7 LYS NZ 99 3.997 -1.476 1.432 + 7 LYS HZ1 100 3.947 -1.49 1.324 + 7 LYS HZ2 101 4.079 -1.562 1.436 + 7 LYS HZ3 102 3.915 -1.522 1.507 + 8 VAL N 103 3.711 -0.799 1.698 + 8 VAL H 104 3.74 -0.877 1.782 + 8 VAL CA 105 3.579 -0.737 1.721 + 8 VAL HA 106 3.509 -0.801 1.649 + 8 VAL C 107 3.578 -0.588 1.689 + 8 VAL O 108 3.478 -0.54 1.626 + 8 VAL CB 109 3.511 -0.76 1.856 + 8 VAL HB 110 3.403 -0.709 1.853 + 8 VAL CG1 111 3.477 -0.905 1.885 + 8 VAL HG11 112 3.374 -0.938 1.833 + 8 VAL HG12 113 3.446 -0.933 1.998 + 8 VAL HG13 114 3.542 -1.003 1.859 + 8 VAL CG2 115 3.577 -0.697 1.973 + 8 VAL HG21 116 3.647 -0.776 2.028 + 8 VAL HG22 117 3.607 -0.582 1.984 + 8 VAL HG23 118 3.493 -0.69 2.059 + 9 LEU N 119 3.686 -0.518 1.722 + 9 LEU H 120 3.786 -0.541 1.778 + 9 LEU CA 121 3.69 -0.376 1.673 + 9 LEU HA 122 3.603 -0.302 1.705 + 9 LEU C 123 3.678 -0.364 1.525 + 9 LEU O 124 3.633 -0.255 1.469 + 9 LEU CB 125 3.823 -0.309 1.715 + 9 LEU HB2 126 3.919 -0.338 1.65 + 9 LEU HB3 127 3.814 -0.196 1.676 + 9 LEU CG 128 3.846 -0.309 1.861 + 9 LEU HG 129 3.875 -0.395 1.938 + 9 LEU CD1 130 3.978 -0.229 1.887 + 9 LEU HD11 131 4.086 -0.278 1.908 + 9 LEU HD12 132 3.974 -0.158 1.985 + 9 LEU HD13 133 4.01 -0.142 1.81 + 9 LEU CD2 134 3.726 -0.254 1.935 + 9 LEU HD21 135 3.712 -0.138 1.907 + 9 LEU HD22 136 3.622 -0.309 1.952 + 9 LEU HD23 137 3.748 -0.235 2.052 + 10 THR N 138 3.732 -0.463 1.453 + 10 THR H 139 3.784 -0.562 1.488 + 10 THR CA 140 3.734 -0.451 1.308 + 10 THR HA 141 3.744 -0.339 1.268 + 10 THR C 142 3.607 -0.502 1.246 + 10 THR O 143 3.569 -0.455 1.133 + 10 THR CB 144 3.869 -0.518 1.249 + 10 THR HB 145 3.887 -0.471 1.14 + 10 THR OG1 146 3.828 -0.654 1.235 + 10 THR HG1 147 3.902 -0.709 1.16 + 10 THR CG2 148 3.988 -0.505 1.345 + 10 THR HG21 149 4.053 -0.574 1.418 + 10 THR HG22 150 4.072 -0.519 1.259 + 10 THR HG23 151 4.003 -0.388 1.364 + 11 THR N 152 3.531 -0.587 1.311 + 11 THR H 153 3.54 -0.636 1.418 + 11 THR CA 154 3.413 -0.641 1.234 + 11 THR HA 155 3.378 -0.595 1.13 + 11 THR C 156 3.287 -0.63 1.314 + 11 THR O 157 3.182 -0.589 1.263 + 11 THR CB 158 3.446 -0.793 1.194 + 11 THR HB 159 3.351 -0.848 1.148 + 11 THR OG1 160 3.47 -0.859 1.32 + 11 THR HG1 161 3.475 -0.976 1.302 + 11 THR CG2 162 3.569 -0.796 1.105 + 11 THR HG21 163 3.517 -0.796 0.996 + 11 THR HG22 164 3.66 -0.726 1.07 + 11 THR HG23 165 3.621 -0.904 1.105 + 12 GLY N 166 3.292 -0.661 1.442 + 12 GLY H 167 3.32 -0.772 1.474 + 12 GLY CA 168 3.158 -0.659 1.514 + 12 GLY HA2 169 3.143 -0.724 1.614 + 12 GLY HA3 170 3.067 -0.704 1.45 + 12 GLY C 171 3.126 -0.517 1.558 + 12 GLY O 172 3.006 -0.491 1.56 + 13 LEU N 173 3.219 -0.428 1.595 + 13 LEU H 174 3.247 -0.488 1.693 + 13 LEU CA 175 3.192 -0.292 1.636 + 13 LEU HA 176 3.1 -0.309 1.71 + 13 LEU C 177 3.125 -0.2 1.532 + 13 LEU O 178 3.023 -0.131 1.568 + 13 LEU CB 179 3.315 -0.218 1.701 + 13 LEU HB2 180 3.386 -0.307 1.733 + 13 LEU HB3 181 3.35 -0.124 1.638 + 13 LEU CG 182 3.291 -0.152 1.835 + 13 LEU HG 183 3.288 -0.231 1.925 + 13 LEU CD1 184 3.4 -0.052 1.876 + 13 LEU HD11 185 3.497 -0.029 1.809 + 13 LEU HD12 186 3.366 0.063 1.885 + 13 LEU HD13 187 3.437 -0.068 1.989 + 13 LEU CD2 188 3.159 -0.084 1.853 + 13 LEU HD21 189 3.15 -0.02 1.954 + 13 LEU HD22 190 3.126 0.0 1.775 + 13 LEU HD23 191 3.061 -0.15 1.877 + 14 PRO N 192 3.169 -0.198 1.411 + 14 PRO CA 193 3.103 -0.128 1.303 + 14 PRO HA 194 3.097 -0.01 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0.545743E+00 +0.784304E+00 0.936113E+00 0.459918E+00 +0.983039E+00 0.747093E+00 0.137667E-02 +0.815739E+00 0.915572E+00 0.458737E+00 +0.809499E+00 0.937816E+00 0.333302E+00 +0.965914E+00 0.762021E+00 0.252445E+00 +0.943312E+00 0.794870E+00 0.380930E+00 +0.924437E+00 0.819165E+00 0.402452E+00 +0.853591E+00 0.905143E+00 0.341284E+00 +0.834249E+00 0.919286E+00 0.344424E+00 +0.766891E+00 0.929200E+00 0.548487E+00 diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/2mlt_frag1/charge.txt b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/2mlt_frag1/charge.txt new file mode 100644 index 00000000..02a7c48a --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/2mlt_frag1/charge.txt @@ -0,0 +1,14 @@ +0 0.0 +1 0.0 +2 0.0 +3 0.0 +4 0.0 +5 0.0 +6 1.0 +7 0.0 +8 0.0 +9 0.0 +10 0.0 +11 0.0 +12 0.0 +13 0.0 diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/2mlt_frag1/cleaned_pdbs/2mlt_frag1.pdb b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/2mlt_frag1/cleaned_pdbs/2mlt_frag1.pdb new file mode 100644 index 00000000..4f7baad3 --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/2mlt_frag1/cleaned_pdbs/2mlt_frag1.pdb @@ -0,0 +1,210 @@ +REMARK 1 CREATED WITH OPENMM 8.1.1, 2025-12-23 +CRYST1 60.832 38.293 42.211 90.00 90.00 90.00 P 1 1 +ATOM 1 N GLY A 1 42.375 -12.180 24.780 1.00 0.00 N +ATOM 2 H GLY A 1 41.348 -11.623 25.042 1.00 0.00 H +ATOM 3 H2 GLY A 1 42.555 -12.690 25.854 1.00 0.00 H +ATOM 4 H3 GLY A 1 42.134 -13.162 24.137 1.00 0.00 H +ATOM 5 CA GLY A 1 43.603 -11.488 24.325 1.00 0.00 C +ATOM 6 HA2 GLY A 1 44.221 -11.213 25.312 1.00 0.00 H +ATOM 7 HA3 GLY A 1 44.301 -12.238 23.709 1.00 0.00 H +ATOM 8 C GLY A 1 43.288 -10.171 23.615 1.00 0.00 C +ATOM 9 O GLY A 1 42.111 -9.896 23.277 1.00 0.00 O +ATOM 10 N ILE A 2 44.323 -9.391 23.299 1.00 0.00 N +ATOM 11 H ILE A 2 45.380 -9.782 23.682 1.00 0.00 H +ATOM 12 CA ILE A 2 44.200 -8.183 22.475 1.00 0.00 C +ATOM 13 HA ILE A 2 43.338 -7.478 22.886 1.00 0.00 H +ATOM 14 C ILE A 2 43.750 -8.629 21.119 1.00 0.00 C +ATOM 15 O ILE A 2 43.068 -7.904 20.409 1.00 0.00 O +ATOM 16 CB ILE A 2 45.525 -7.320 22.425 1.00 0.00 C +ATOM 17 HB ILE A 2 46.450 -7.997 22.088 1.00 0.00 H +ATOM 18 CG1 ILE A 2 45.924 -6.837 23.820 1.00 0.00 C +ATOM 19 HG12 ILE A 2 46.792 -6.010 23.800 1.00 0.00 H +ATOM 20 HG13 ILE A 2 46.531 -7.674 24.425 1.00 0.00 H +ATOM 21 CG2 ILE A 2 45.555 -6.173 21.386 1.00 0.00 C +ATOM 22 HG21 ILE A 2 44.588 -5.494 21.214 1.00 0.00 H +ATOM 23 HG22 ILE A 2 46.339 -5.297 21.634 1.00 0.00 H +ATOM 24 HG23 ILE A 2 46.069 -6.532 20.365 1.00 0.00 H +ATOM 25 CD1 ILE A 2 44.837 -6.338 24.762 1.00 0.00 C +ATOM 26 HD11 ILE A 2 45.139 -5.222 25.094 1.00 0.00 H +ATOM 27 HD12 ILE A 2 44.872 -6.908 25.818 1.00 0.00 H +ATOM 28 HD13 ILE A 2 43.661 -6.128 24.665 1.00 0.00 H +ATOM 29 N GLY A 3 44.161 -9.867 20.749 1.00 0.00 N +ATOM 30 H GLY A 3 45.133 -10.465 21.085 1.00 0.00 H +ATOM 31 CA GLY A 3 43.999 -10.264 19.329 1.00 0.00 C +ATOM 32 HA2 GLY A 3 44.702 -9.646 18.587 1.00 0.00 H +ATOM 33 HA3 GLY A 3 44.390 -11.358 19.035 1.00 0.00 H +ATOM 34 C GLY A 3 42.433 -10.405 19.166 1.00 0.00 C +ATOM 35 O GLY A 3 41.912 -10.061 18.096 1.00 0.00 O +ATOM 36 N ALA A 4 41.862 -10.961 20.191 1.00 0.00 N +ATOM 37 H ALA A 4 42.465 -11.922 20.552 1.00 0.00 H +ATOM 38 CA ALA A 4 40.378 -11.260 20.106 1.00 0.00 C +ATOM 39 HA ALA A 4 40.148 -11.961 19.170 1.00 0.00 H +ATOM 40 C ALA A 4 39.584 -9.950 20.087 1.00 0.00 C +ATOM 41 O ALA A 4 38.676 -9.747 19.278 1.00 0.00 O +ATOM 42 CB ALA A 4 40.061 -12.080 21.350 1.00 0.00 C +ATOM 43 HB1 ALA A 4 39.843 -11.708 22.467 1.00 0.00 H +ATOM 44 HB2 ALA A 4 40.636 -13.124 21.485 1.00 0.00 H +ATOM 45 HB3 ALA A 4 38.960 -12.518 21.142 1.00 0.00 H +ATOM 46 N VAL A 5 39.936 -9.001 20.956 1.00 0.00 N +ATOM 47 H VAL A 5 40.629 -9.354 21.844 1.00 0.00 H +ATOM 48 CA VAL A 5 39.355 -7.658 21.083 1.00 0.00 C +ATOM 49 HA VAL A 5 38.259 -7.965 21.431 1.00 0.00 H +ATOM 50 C VAL A 5 39.536 -6.896 19.795 1.00 0.00 C +ATOM 51 O VAL A 5 38.626 -6.314 19.126 1.00 0.00 O +ATOM 52 CB VAL A 5 39.843 -6.933 22.338 1.00 0.00 C +ATOM 53 HB VAL A 5 40.988 -6.605 22.371 1.00 0.00 H +ATOM 54 CG1 VAL A 5 39.237 -5.519 22.413 1.00 0.00 C +ATOM 55 HG11 VAL A 5 38.051 -5.502 22.584 1.00 0.00 H +ATOM 56 HG12 VAL A 5 39.563 -4.681 21.625 1.00 0.00 H +ATOM 57 HG13 VAL A 5 39.559 -4.865 23.372 1.00 0.00 H +ATOM 58 CG2 VAL A 5 39.745 -7.587 23.653 1.00 0.00 C +ATOM 59 HG21 VAL A 5 39.713 -6.840 24.597 1.00 0.00 H +ATOM 60 HG22 VAL A 5 38.700 -8.144 23.855 1.00 0.00 H +ATOM 61 HG23 VAL A 5 40.504 -8.343 24.190 1.00 0.00 H +ATOM 62 N LEU A 6 40.752 -7.021 19.222 1.00 0.00 N +ATOM 63 H LEU A 6 41.432 -6.456 20.018 1.00 0.00 H +ATOM 64 CA LEU A 6 41.062 -6.432 17.957 1.00 0.00 C +ATOM 65 HA LEU A 6 40.866 -5.262 18.044 1.00 0.00 H +ATOM 66 C LEU A 6 40.230 -6.935 16.870 1.00 0.00 C +ATOM 67 O LEU A 6 39.649 -6.121 16.029 1.00 0.00 O +ATOM 68 CB LEU A 6 42.627 -6.461 17.880 1.00 0.00 C +ATOM 69 HB2 LEU A 6 43.172 -5.759 18.678 1.00 0.00 H +ATOM 70 HB3 LEU A 6 42.971 -7.600 17.910 1.00 0.00 H +ATOM 71 CG LEU A 6 43.125 -6.023 16.524 1.00 0.00 C +ATOM 72 HG LEU A 6 42.903 -6.713 15.576 1.00 0.00 H +ATOM 73 CD1 LEU A 6 42.706 -4.584 16.210 1.00 0.00 C +ATOM 74 HD11 LEU A 6 43.272 -4.298 15.188 1.00 0.00 H +ATOM 75 HD12 LEU A 6 43.196 -3.769 16.945 1.00 0.00 H +ATOM 76 HD13 LEU A 6 41.687 -4.015 15.951 1.00 0.00 H +ATOM 77 CD2 LEU A 6 44.669 -6.152 16.638 1.00 0.00 C +ATOM 78 HD21 LEU A 6 45.189 -5.937 15.574 1.00 0.00 H +ATOM 79 HD22 LEU A 6 45.323 -5.404 17.311 1.00 0.00 H +ATOM 80 HD23 LEU A 6 45.194 -7.216 16.816 1.00 0.00 H +ATOM 81 N LYS A 7 39.981 -8.229 16.721 1.00 0.00 N +ATOM 82 H LYS A 7 40.772 -9.075 16.935 1.00 0.00 H +ATOM 83 CA LYS A 7 39.079 -8.646 15.636 1.00 0.00 C +ATOM 84 HA LYS A 7 39.583 -8.378 14.590 1.00 0.00 H +ATOM 85 C LYS A 7 37.648 -8.063 15.784 1.00 0.00 C +ATOM 86 O LYS A 7 37.031 -7.839 14.731 1.00 0.00 O +ATOM 87 CB LYS A 7 38.854 -10.176 15.616 1.00 0.00 C +ATOM 88 HB2 LYS A 7 37.977 -10.374 14.825 1.00 0.00 H +ATOM 89 HB3 LYS A 7 38.398 -10.663 16.606 1.00 0.00 H +ATOM 90 CG LYS A 7 40.011 -10.993 15.144 1.00 0.00 C +ATOM 91 HG2 LYS A 7 41.158 -10.886 15.464 1.00 0.00 H +ATOM 92 HG3 LYS A 7 40.110 -10.782 13.968 1.00 0.00 H +ATOM 93 CD LYS A 7 39.691 -12.487 15.325 1.00 0.00 C +ATOM 94 HD2 LYS A 7 39.801 -12.898 16.441 1.00 0.00 H +ATOM 95 HD3 LYS A 7 38.586 -12.748 14.951 1.00 0.00 H +ATOM 96 CE LYS A 7 40.599 -13.394 14.493 1.00 0.00 C +ATOM 97 HE2 LYS A 7 41.676 -13.535 14.991 1.00 0.00 H +ATOM 98 HE3 LYS A 7 40.872 -13.049 13.380 1.00 0.00 H +ATOM 99 NZ LYS A 7 39.966 -14.755 14.319 1.00 0.00 N +ATOM 100 HZ1 LYS A 7 39.465 -14.898 13.239 1.00 0.00 H +ATOM 101 HZ2 LYS A 7 40.794 -15.623 14.363 1.00 0.00 H +ATOM 102 HZ3 LYS A 7 39.153 -15.222 15.066 1.00 0.00 H +ATOM 103 N VAL A 8 37.111 -7.988 16.981 1.00 0.00 N +ATOM 104 H VAL A 8 37.403 -8.767 17.821 1.00 0.00 H +ATOM 105 CA VAL A 8 35.792 -7.369 17.211 1.00 0.00 C +ATOM 106 HA VAL A 8 35.091 -8.010 16.491 1.00 0.00 H +ATOM 107 C VAL A 8 35.776 -5.881 16.885 1.00 0.00 C +ATOM 108 O VAL A 8 34.775 -5.402 16.257 1.00 0.00 O +ATOM 109 CB VAL A 8 35.113 -7.600 18.562 1.00 0.00 C +ATOM 110 HB VAL A 8 34.034 -7.086 18.529 1.00 0.00 H +ATOM 111 CG1 VAL A 8 34.774 -9.045 18.851 1.00 0.00 C +ATOM 112 HG11 VAL A 8 33.742 -9.377 18.329 1.00 0.00 H +ATOM 113 HG12 VAL A 8 34.457 -9.332 19.975 1.00 0.00 H +ATOM 114 HG13 VAL A 8 35.415 -10.026 18.593 1.00 0.00 H +ATOM 115 CG2 VAL A 8 35.769 -6.970 19.726 1.00 0.00 C +ATOM 116 HG21 VAL A 8 36.472 -7.757 20.279 1.00 0.00 H +ATOM 117 HG22 VAL A 8 36.066 -5.819 19.842 1.00 0.00 H +ATOM 118 HG23 VAL A 8 34.929 -6.899 20.590 1.00 0.00 H +ATOM 119 N LEU A 9 36.860 -5.176 17.216 1.00 0.00 N +ATOM 120 H LEU A 9 37.858 -5.414 17.783 1.00 0.00 H +ATOM 121 CA LEU A 9 36.899 -3.759 16.725 1.00 0.00 C +ATOM 122 HA LEU A 9 36.033 -3.017 17.052 1.00 0.00 H +ATOM 123 C LEU A 9 36.778 -3.644 15.254 1.00 0.00 C +ATOM 124 O LEU A 9 36.328 -2.551 14.694 1.00 0.00 O +ATOM 125 CB LEU A 9 38.227 -3.088 17.147 1.00 0.00 C +ATOM 126 HB2 LEU A 9 39.189 -3.378 16.504 1.00 0.00 H +ATOM 127 HB3 LEU A 9 38.137 -1.956 16.758 1.00 0.00 H +ATOM 128 CG LEU A 9 38.462 -3.091 18.615 1.00 0.00 C +ATOM 129 HG LEU A 9 38.754 -3.955 19.375 1.00 0.00 H +ATOM 130 CD1 LEU A 9 39.783 -2.288 18.873 1.00 0.00 C +ATOM 131 HD11 LEU A 9 40.856 -2.781 19.080 1.00 0.00 H +ATOM 132 HD12 LEU A 9 39.745 -1.582 19.847 1.00 0.00 H +ATOM 133 HD13 LEU A 9 40.098 -1.424 18.099 1.00 0.00 H +ATOM 134 CD2 LEU A 9 37.265 -2.535 19.351 1.00 0.00 C +ATOM 135 HD21 LEU A 9 37.115 -1.380 19.067 1.00 0.00 H +ATOM 136 HD22 LEU A 9 36.218 -3.088 19.520 1.00 0.00 H +ATOM 137 HD23 LEU A 9 37.478 -2.347 20.522 1.00 0.00 H +ATOM 138 N THR A 10 37.320 -4.627 14.530 1.00 0.00 N +ATOM 139 H THR A 10 37.840 -5.625 14.880 1.00 0.00 H +ATOM 140 CA THR A 10 37.338 -4.508 13.084 1.00 0.00 C +ATOM 141 HA THR A 10 37.440 -3.390 12.679 1.00 0.00 H +ATOM 142 C THR A 10 36.072 -5.022 12.458 1.00 0.00 C +ATOM 143 O THR A 10 35.694 -4.554 11.333 1.00 0.00 O +ATOM 144 CB THR A 10 38.687 -5.179 12.486 1.00 0.00 C +ATOM 145 HB THR A 10 38.867 -4.707 11.403 1.00 0.00 H +ATOM 146 OG1 THR A 10 38.285 -6.538 12.354 1.00 0.00 O +ATOM 147 HG1 THR A 10 39.022 -7.085 11.599 1.00 0.00 H +ATOM 148 CG2 THR A 10 39.877 -5.049 13.451 1.00 0.00 C +ATOM 149 HG21 THR A 10 40.525 -5.741 14.176 1.00 0.00 H +ATOM 150 HG22 THR A 10 40.717 -5.188 12.594 1.00 0.00 H +ATOM 151 HG23 THR A 10 40.027 -3.875 13.642 1.00 0.00 H +ATOM 152 N THR A 11 35.315 -5.870 13.113 1.00 0.00 N +ATOM 153 H THR A 11 35.402 -6.359 14.181 1.00 0.00 H +ATOM 154 CA THR A 11 34.132 -6.405 12.343 1.00 0.00 C +ATOM 155 HA THR A 11 33.776 -5.952 11.299 1.00 0.00 H +ATOM 156 C THR A 11 32.874 -6.299 13.140 1.00 0.00 C +ATOM 157 O THR A 11 31.823 -5.889 12.630 1.00 0.00 O +ATOM 158 CB THR A 11 34.462 -7.925 11.935 1.00 0.00 C +ATOM 159 HB THR A 11 33.509 -8.482 11.478 1.00 0.00 H +ATOM 160 OG1 THR A 11 34.702 -8.591 13.199 1.00 0.00 O +ATOM 161 HG1 THR A 11 34.748 -9.764 13.020 1.00 0.00 H +ATOM 162 CG2 THR A 11 35.695 -7.959 11.047 1.00 0.00 C +ATOM 163 HG21 THR A 11 35.174 -7.957 9.962 1.00 0.00 H +ATOM 164 HG22 THR A 11 36.601 -7.258 10.698 1.00 0.00 H +ATOM 165 HG23 THR A 11 36.212 -9.042 11.053 1.00 0.00 H +ATOM 166 N GLY A 12 32.918 -6.606 14.420 1.00 0.00 N +ATOM 167 H GLY A 12 33.201 -7.715 14.741 1.00 0.00 H +ATOM 168 CA GLY A 12 31.584 -6.595 15.140 1.00 0.00 C +ATOM 169 HA2 GLY A 12 31.429 -7.241 16.136 1.00 0.00 H +ATOM 170 HA3 GLY A 12 30.674 -7.036 14.498 1.00 0.00 H +ATOM 171 C GLY A 12 31.264 -5.168 15.584 1.00 0.00 C +ATOM 172 O GLY A 12 30.060 -4.914 15.603 1.00 0.00 O +ATOM 173 N LEU A 13 32.195 -4.276 15.948 1.00 0.00 N +ATOM 174 H LEU A 13 32.473 -4.884 16.934 1.00 0.00 H +ATOM 175 CA LEU A 13 31.923 -2.919 16.364 1.00 0.00 C +ATOM 176 HA LEU A 13 30.998 -3.094 17.098 1.00 0.00 H +ATOM 177 C LEU A 13 31.251 -2.004 15.324 1.00 0.00 C +ATOM 178 O LEU A 13 30.232 -1.308 15.679 1.00 0.00 O +ATOM 179 CB LEU A 13 33.146 -2.183 17.008 1.00 0.00 C +ATOM 180 HB2 LEU A 13 33.863 -3.073 17.325 1.00 0.00 H +ATOM 181 HB3 LEU A 13 33.501 -1.235 16.375 1.00 0.00 H +ATOM 182 CG LEU A 13 32.913 -1.523 18.351 1.00 0.00 C +ATOM 183 HG LEU A 13 32.879 -2.314 19.248 1.00 0.00 H +ATOM 184 CD1 LEU A 13 33.999 -0.517 18.760 1.00 0.00 C +ATOM 185 HD11 LEU A 13 34.965 -0.295 18.088 1.00 0.00 H +ATOM 186 HD12 LEU A 13 33.658 0.633 18.847 1.00 0.00 H +ATOM 187 HD13 LEU A 13 34.370 -0.681 19.889 1.00 0.00 H +ATOM 188 CD2 LEU A 13 31.587 -0.842 18.531 1.00 0.00 C +ATOM 189 HD21 LEU A 13 31.499 -0.196 19.543 1.00 0.00 H +ATOM 190 HD22 LEU A 13 31.256 0.004 17.748 1.00 0.00 H +ATOM 191 HD23 LEU A 13 30.609 -1.496 18.772 1.00 0.00 H +ATOM 192 N PRO A 14 31.689 -1.979 14.106 1.00 0.00 N +ATOM 193 CA PRO A 14 31.026 -1.278 13.030 1.00 0.00 C +ATOM 194 HA PRO A 14 30.971 -0.101 13.220 1.00 0.00 H +ATOM 195 C PRO A 14 29.521 -1.670 12.857 1.00 0.00 C +ATOM 196 O PRO A 14 28.657 -0.801 12.744 1.00 0.00 O +ATOM 197 CB PRO A 14 31.845 -1.614 11.816 1.00 0.00 C +ATOM 198 HB2 PRO A 14 31.257 -2.227 10.972 1.00 0.00 H +ATOM 199 HB3 PRO A 14 32.036 -0.613 11.183 1.00 0.00 H +ATOM 200 CG PRO A 14 33.118 -2.205 12.303 1.00 0.00 C +ATOM 201 HG2 PRO A 14 33.250 -3.166 11.606 1.00 0.00 H +ATOM 202 HG3 PRO A 14 34.010 -1.511 11.899 1.00 0.00 H +ATOM 203 CD PRO A 14 33.098 -2.363 13.769 1.00 0.00 C +ATOM 204 HD2 PRO A 14 33.564 -3.425 14.021 1.00 0.00 H +ATOM 205 HD3 PRO A 14 33.775 -1.449 14.137 1.00 0.00 H +ATOM 206 OXT PRO A 14 29.767 -2.895 12.875 1.00 0.00 O +TER 207 PRO A 14 +END diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/2mlt_frag1/crystal_structure-cleaned.pdb b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/2mlt_frag1/crystal_structure-cleaned.pdb new file mode 100644 index 00000000..4f7baad3 --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/2mlt_frag1/crystal_structure-cleaned.pdb @@ -0,0 +1,210 @@ +REMARK 1 CREATED WITH OPENMM 8.1.1, 2025-12-23 +CRYST1 60.832 38.293 42.211 90.00 90.00 90.00 P 1 1 +ATOM 1 N GLY A 1 42.375 -12.180 24.780 1.00 0.00 N +ATOM 2 H GLY A 1 41.348 -11.623 25.042 1.00 0.00 H +ATOM 3 H2 GLY A 1 42.555 -12.690 25.854 1.00 0.00 H +ATOM 4 H3 GLY A 1 42.134 -13.162 24.137 1.00 0.00 H +ATOM 5 CA GLY A 1 43.603 -11.488 24.325 1.00 0.00 C +ATOM 6 HA2 GLY A 1 44.221 -11.213 25.312 1.00 0.00 H +ATOM 7 HA3 GLY A 1 44.301 -12.238 23.709 1.00 0.00 H +ATOM 8 C GLY A 1 43.288 -10.171 23.615 1.00 0.00 C +ATOM 9 O GLY A 1 42.111 -9.896 23.277 1.00 0.00 O +ATOM 10 N ILE A 2 44.323 -9.391 23.299 1.00 0.00 N +ATOM 11 H ILE A 2 45.380 -9.782 23.682 1.00 0.00 H +ATOM 12 CA ILE A 2 44.200 -8.183 22.475 1.00 0.00 C +ATOM 13 HA ILE A 2 43.338 -7.478 22.886 1.00 0.00 H +ATOM 14 C ILE A 2 43.750 -8.629 21.119 1.00 0.00 C +ATOM 15 O ILE A 2 43.068 -7.904 20.409 1.00 0.00 O +ATOM 16 CB ILE A 2 45.525 -7.320 22.425 1.00 0.00 C +ATOM 17 HB ILE A 2 46.450 -7.997 22.088 1.00 0.00 H +ATOM 18 CG1 ILE A 2 45.924 -6.837 23.820 1.00 0.00 C +ATOM 19 HG12 ILE A 2 46.792 -6.010 23.800 1.00 0.00 H +ATOM 20 HG13 ILE A 2 46.531 -7.674 24.425 1.00 0.00 H +ATOM 21 CG2 ILE A 2 45.555 -6.173 21.386 1.00 0.00 C +ATOM 22 HG21 ILE A 2 44.588 -5.494 21.214 1.00 0.00 H +ATOM 23 HG22 ILE A 2 46.339 -5.297 21.634 1.00 0.00 H +ATOM 24 HG23 ILE A 2 46.069 -6.532 20.365 1.00 0.00 H +ATOM 25 CD1 ILE A 2 44.837 -6.338 24.762 1.00 0.00 C +ATOM 26 HD11 ILE A 2 45.139 -5.222 25.094 1.00 0.00 H +ATOM 27 HD12 ILE A 2 44.872 -6.908 25.818 1.00 0.00 H +ATOM 28 HD13 ILE A 2 43.661 -6.128 24.665 1.00 0.00 H +ATOM 29 N GLY A 3 44.161 -9.867 20.749 1.00 0.00 N +ATOM 30 H GLY A 3 45.133 -10.465 21.085 1.00 0.00 H +ATOM 31 CA GLY A 3 43.999 -10.264 19.329 1.00 0.00 C +ATOM 32 HA2 GLY A 3 44.702 -9.646 18.587 1.00 0.00 H +ATOM 33 HA3 GLY A 3 44.390 -11.358 19.035 1.00 0.00 H +ATOM 34 C GLY A 3 42.433 -10.405 19.166 1.00 0.00 C +ATOM 35 O GLY A 3 41.912 -10.061 18.096 1.00 0.00 O +ATOM 36 N ALA A 4 41.862 -10.961 20.191 1.00 0.00 N +ATOM 37 H ALA A 4 42.465 -11.922 20.552 1.00 0.00 H +ATOM 38 CA ALA A 4 40.378 -11.260 20.106 1.00 0.00 C +ATOM 39 HA ALA A 4 40.148 -11.961 19.170 1.00 0.00 H +ATOM 40 C ALA A 4 39.584 -9.950 20.087 1.00 0.00 C +ATOM 41 O ALA A 4 38.676 -9.747 19.278 1.00 0.00 O +ATOM 42 CB ALA A 4 40.061 -12.080 21.350 1.00 0.00 C +ATOM 43 HB1 ALA A 4 39.843 -11.708 22.467 1.00 0.00 H +ATOM 44 HB2 ALA A 4 40.636 -13.124 21.485 1.00 0.00 H +ATOM 45 HB3 ALA A 4 38.960 -12.518 21.142 1.00 0.00 H +ATOM 46 N VAL A 5 39.936 -9.001 20.956 1.00 0.00 N +ATOM 47 H VAL A 5 40.629 -9.354 21.844 1.00 0.00 H +ATOM 48 CA VAL A 5 39.355 -7.658 21.083 1.00 0.00 C +ATOM 49 HA VAL A 5 38.259 -7.965 21.431 1.00 0.00 H +ATOM 50 C VAL A 5 39.536 -6.896 19.795 1.00 0.00 C +ATOM 51 O VAL A 5 38.626 -6.314 19.126 1.00 0.00 O +ATOM 52 CB VAL A 5 39.843 -6.933 22.338 1.00 0.00 C +ATOM 53 HB VAL A 5 40.988 -6.605 22.371 1.00 0.00 H +ATOM 54 CG1 VAL A 5 39.237 -5.519 22.413 1.00 0.00 C +ATOM 55 HG11 VAL A 5 38.051 -5.502 22.584 1.00 0.00 H +ATOM 56 HG12 VAL A 5 39.563 -4.681 21.625 1.00 0.00 H +ATOM 57 HG13 VAL A 5 39.559 -4.865 23.372 1.00 0.00 H +ATOM 58 CG2 VAL A 5 39.745 -7.587 23.653 1.00 0.00 C +ATOM 59 HG21 VAL A 5 39.713 -6.840 24.597 1.00 0.00 H +ATOM 60 HG22 VAL A 5 38.700 -8.144 23.855 1.00 0.00 H +ATOM 61 HG23 VAL A 5 40.504 -8.343 24.190 1.00 0.00 H +ATOM 62 N LEU A 6 40.752 -7.021 19.222 1.00 0.00 N +ATOM 63 H LEU A 6 41.432 -6.456 20.018 1.00 0.00 H +ATOM 64 CA LEU A 6 41.062 -6.432 17.957 1.00 0.00 C +ATOM 65 HA LEU A 6 40.866 -5.262 18.044 1.00 0.00 H +ATOM 66 C LEU A 6 40.230 -6.935 16.870 1.00 0.00 C +ATOM 67 O LEU A 6 39.649 -6.121 16.029 1.00 0.00 O +ATOM 68 CB LEU A 6 42.627 -6.461 17.880 1.00 0.00 C +ATOM 69 HB2 LEU A 6 43.172 -5.759 18.678 1.00 0.00 H +ATOM 70 HB3 LEU A 6 42.971 -7.600 17.910 1.00 0.00 H +ATOM 71 CG LEU A 6 43.125 -6.023 16.524 1.00 0.00 C +ATOM 72 HG LEU A 6 42.903 -6.713 15.576 1.00 0.00 H +ATOM 73 CD1 LEU A 6 42.706 -4.584 16.210 1.00 0.00 C +ATOM 74 HD11 LEU A 6 43.272 -4.298 15.188 1.00 0.00 H +ATOM 75 HD12 LEU A 6 43.196 -3.769 16.945 1.00 0.00 H +ATOM 76 HD13 LEU A 6 41.687 -4.015 15.951 1.00 0.00 H +ATOM 77 CD2 LEU A 6 44.669 -6.152 16.638 1.00 0.00 C +ATOM 78 HD21 LEU A 6 45.189 -5.937 15.574 1.00 0.00 H +ATOM 79 HD22 LEU A 6 45.323 -5.404 17.311 1.00 0.00 H +ATOM 80 HD23 LEU A 6 45.194 -7.216 16.816 1.00 0.00 H +ATOM 81 N LYS A 7 39.981 -8.229 16.721 1.00 0.00 N +ATOM 82 H LYS A 7 40.772 -9.075 16.935 1.00 0.00 H +ATOM 83 CA LYS A 7 39.079 -8.646 15.636 1.00 0.00 C +ATOM 84 HA LYS A 7 39.583 -8.378 14.590 1.00 0.00 H +ATOM 85 C LYS A 7 37.648 -8.063 15.784 1.00 0.00 C +ATOM 86 O LYS A 7 37.031 -7.839 14.731 1.00 0.00 O +ATOM 87 CB LYS A 7 38.854 -10.176 15.616 1.00 0.00 C +ATOM 88 HB2 LYS A 7 37.977 -10.374 14.825 1.00 0.00 H +ATOM 89 HB3 LYS A 7 38.398 -10.663 16.606 1.00 0.00 H +ATOM 90 CG LYS A 7 40.011 -10.993 15.144 1.00 0.00 C +ATOM 91 HG2 LYS A 7 41.158 -10.886 15.464 1.00 0.00 H +ATOM 92 HG3 LYS A 7 40.110 -10.782 13.968 1.00 0.00 H +ATOM 93 CD LYS A 7 39.691 -12.487 15.325 1.00 0.00 C +ATOM 94 HD2 LYS A 7 39.801 -12.898 16.441 1.00 0.00 H +ATOM 95 HD3 LYS A 7 38.586 -12.748 14.951 1.00 0.00 H +ATOM 96 CE LYS A 7 40.599 -13.394 14.493 1.00 0.00 C +ATOM 97 HE2 LYS A 7 41.676 -13.535 14.991 1.00 0.00 H +ATOM 98 HE3 LYS A 7 40.872 -13.049 13.380 1.00 0.00 H +ATOM 99 NZ LYS A 7 39.966 -14.755 14.319 1.00 0.00 N +ATOM 100 HZ1 LYS A 7 39.465 -14.898 13.239 1.00 0.00 H +ATOM 101 HZ2 LYS A 7 40.794 -15.623 14.363 1.00 0.00 H +ATOM 102 HZ3 LYS A 7 39.153 -15.222 15.066 1.00 0.00 H +ATOM 103 N VAL A 8 37.111 -7.988 16.981 1.00 0.00 N +ATOM 104 H VAL A 8 37.403 -8.767 17.821 1.00 0.00 H +ATOM 105 CA VAL A 8 35.792 -7.369 17.211 1.00 0.00 C +ATOM 106 HA VAL A 8 35.091 -8.010 16.491 1.00 0.00 H +ATOM 107 C VAL A 8 35.776 -5.881 16.885 1.00 0.00 C +ATOM 108 O VAL A 8 34.775 -5.402 16.257 1.00 0.00 O +ATOM 109 CB VAL A 8 35.113 -7.600 18.562 1.00 0.00 C +ATOM 110 HB VAL A 8 34.034 -7.086 18.529 1.00 0.00 H +ATOM 111 CG1 VAL A 8 34.774 -9.045 18.851 1.00 0.00 C +ATOM 112 HG11 VAL A 8 33.742 -9.377 18.329 1.00 0.00 H +ATOM 113 HG12 VAL A 8 34.457 -9.332 19.975 1.00 0.00 H +ATOM 114 HG13 VAL A 8 35.415 -10.026 18.593 1.00 0.00 H +ATOM 115 CG2 VAL A 8 35.769 -6.970 19.726 1.00 0.00 C +ATOM 116 HG21 VAL A 8 36.472 -7.757 20.279 1.00 0.00 H +ATOM 117 HG22 VAL A 8 36.066 -5.819 19.842 1.00 0.00 H +ATOM 118 HG23 VAL A 8 34.929 -6.899 20.590 1.00 0.00 H +ATOM 119 N LEU A 9 36.860 -5.176 17.216 1.00 0.00 N +ATOM 120 H LEU A 9 37.858 -5.414 17.783 1.00 0.00 H +ATOM 121 CA LEU A 9 36.899 -3.759 16.725 1.00 0.00 C +ATOM 122 HA LEU A 9 36.033 -3.017 17.052 1.00 0.00 H +ATOM 123 C LEU A 9 36.778 -3.644 15.254 1.00 0.00 C +ATOM 124 O LEU A 9 36.328 -2.551 14.694 1.00 0.00 O +ATOM 125 CB LEU A 9 38.227 -3.088 17.147 1.00 0.00 C +ATOM 126 HB2 LEU A 9 39.189 -3.378 16.504 1.00 0.00 H +ATOM 127 HB3 LEU A 9 38.137 -1.956 16.758 1.00 0.00 H +ATOM 128 CG LEU A 9 38.462 -3.091 18.615 1.00 0.00 C +ATOM 129 HG LEU A 9 38.754 -3.955 19.375 1.00 0.00 H +ATOM 130 CD1 LEU A 9 39.783 -2.288 18.873 1.00 0.00 C +ATOM 131 HD11 LEU A 9 40.856 -2.781 19.080 1.00 0.00 H +ATOM 132 HD12 LEU A 9 39.745 -1.582 19.847 1.00 0.00 H +ATOM 133 HD13 LEU A 9 40.098 -1.424 18.099 1.00 0.00 H +ATOM 134 CD2 LEU A 9 37.265 -2.535 19.351 1.00 0.00 C +ATOM 135 HD21 LEU A 9 37.115 -1.380 19.067 1.00 0.00 H +ATOM 136 HD22 LEU A 9 36.218 -3.088 19.520 1.00 0.00 H +ATOM 137 HD23 LEU A 9 37.478 -2.347 20.522 1.00 0.00 H +ATOM 138 N THR A 10 37.320 -4.627 14.530 1.00 0.00 N +ATOM 139 H THR A 10 37.840 -5.625 14.880 1.00 0.00 H +ATOM 140 CA THR A 10 37.338 -4.508 13.084 1.00 0.00 C +ATOM 141 HA THR A 10 37.440 -3.390 12.679 1.00 0.00 H +ATOM 142 C THR A 10 36.072 -5.022 12.458 1.00 0.00 C +ATOM 143 O THR A 10 35.694 -4.554 11.333 1.00 0.00 O +ATOM 144 CB THR A 10 38.687 -5.179 12.486 1.00 0.00 C +ATOM 145 HB THR A 10 38.867 -4.707 11.403 1.00 0.00 H +ATOM 146 OG1 THR A 10 38.285 -6.538 12.354 1.00 0.00 O +ATOM 147 HG1 THR A 10 39.022 -7.085 11.599 1.00 0.00 H +ATOM 148 CG2 THR A 10 39.877 -5.049 13.451 1.00 0.00 C +ATOM 149 HG21 THR A 10 40.525 -5.741 14.176 1.00 0.00 H +ATOM 150 HG22 THR A 10 40.717 -5.188 12.594 1.00 0.00 H +ATOM 151 HG23 THR A 10 40.027 -3.875 13.642 1.00 0.00 H +ATOM 152 N THR A 11 35.315 -5.870 13.113 1.00 0.00 N +ATOM 153 H THR A 11 35.402 -6.359 14.181 1.00 0.00 H +ATOM 154 CA THR A 11 34.132 -6.405 12.343 1.00 0.00 C +ATOM 155 HA THR A 11 33.776 -5.952 11.299 1.00 0.00 H +ATOM 156 C THR A 11 32.874 -6.299 13.140 1.00 0.00 C +ATOM 157 O THR A 11 31.823 -5.889 12.630 1.00 0.00 O +ATOM 158 CB THR A 11 34.462 -7.925 11.935 1.00 0.00 C +ATOM 159 HB THR A 11 33.509 -8.482 11.478 1.00 0.00 H +ATOM 160 OG1 THR A 11 34.702 -8.591 13.199 1.00 0.00 O +ATOM 161 HG1 THR A 11 34.748 -9.764 13.020 1.00 0.00 H +ATOM 162 CG2 THR A 11 35.695 -7.959 11.047 1.00 0.00 C +ATOM 163 HG21 THR A 11 35.174 -7.957 9.962 1.00 0.00 H +ATOM 164 HG22 THR A 11 36.601 -7.258 10.698 1.00 0.00 H +ATOM 165 HG23 THR A 11 36.212 -9.042 11.053 1.00 0.00 H +ATOM 166 N GLY A 12 32.918 -6.606 14.420 1.00 0.00 N +ATOM 167 H GLY A 12 33.201 -7.715 14.741 1.00 0.00 H +ATOM 168 CA GLY A 12 31.584 -6.595 15.140 1.00 0.00 C +ATOM 169 HA2 GLY A 12 31.429 -7.241 16.136 1.00 0.00 H +ATOM 170 HA3 GLY A 12 30.674 -7.036 14.498 1.00 0.00 H +ATOM 171 C GLY A 12 31.264 -5.168 15.584 1.00 0.00 C +ATOM 172 O GLY A 12 30.060 -4.914 15.603 1.00 0.00 O +ATOM 173 N LEU A 13 32.195 -4.276 15.948 1.00 0.00 N +ATOM 174 H LEU A 13 32.473 -4.884 16.934 1.00 0.00 H +ATOM 175 CA LEU A 13 31.923 -2.919 16.364 1.00 0.00 C +ATOM 176 HA LEU A 13 30.998 -3.094 17.098 1.00 0.00 H +ATOM 177 C LEU A 13 31.251 -2.004 15.324 1.00 0.00 C +ATOM 178 O LEU A 13 30.232 -1.308 15.679 1.00 0.00 O +ATOM 179 CB LEU A 13 33.146 -2.183 17.008 1.00 0.00 C +ATOM 180 HB2 LEU A 13 33.863 -3.073 17.325 1.00 0.00 H +ATOM 181 HB3 LEU A 13 33.501 -1.235 16.375 1.00 0.00 H +ATOM 182 CG LEU A 13 32.913 -1.523 18.351 1.00 0.00 C +ATOM 183 HG LEU A 13 32.879 -2.314 19.248 1.00 0.00 H +ATOM 184 CD1 LEU A 13 33.999 -0.517 18.760 1.00 0.00 C +ATOM 185 HD11 LEU A 13 34.965 -0.295 18.088 1.00 0.00 H +ATOM 186 HD12 LEU A 13 33.658 0.633 18.847 1.00 0.00 H +ATOM 187 HD13 LEU A 13 34.370 -0.681 19.889 1.00 0.00 H +ATOM 188 CD2 LEU A 13 31.587 -0.842 18.531 1.00 0.00 C +ATOM 189 HD21 LEU A 13 31.499 -0.196 19.543 1.00 0.00 H +ATOM 190 HD22 LEU A 13 31.256 0.004 17.748 1.00 0.00 H +ATOM 191 HD23 LEU A 13 30.609 -1.496 18.772 1.00 0.00 H +ATOM 192 N PRO A 14 31.689 -1.979 14.106 1.00 0.00 N +ATOM 193 CA PRO A 14 31.026 -1.278 13.030 1.00 0.00 C +ATOM 194 HA PRO A 14 30.971 -0.101 13.220 1.00 0.00 H +ATOM 195 C PRO A 14 29.521 -1.670 12.857 1.00 0.00 C +ATOM 196 O PRO A 14 28.657 -0.801 12.744 1.00 0.00 O +ATOM 197 CB PRO A 14 31.845 -1.614 11.816 1.00 0.00 C +ATOM 198 HB2 PRO A 14 31.257 -2.227 10.972 1.00 0.00 H +ATOM 199 HB3 PRO A 14 32.036 -0.613 11.183 1.00 0.00 H +ATOM 200 CG PRO A 14 33.118 -2.205 12.303 1.00 0.00 C +ATOM 201 HG2 PRO A 14 33.250 -3.166 11.606 1.00 0.00 H +ATOM 202 HG3 PRO A 14 34.010 -1.511 11.899 1.00 0.00 H +ATOM 203 CD PRO A 14 33.098 -2.363 13.769 1.00 0.00 C +ATOM 204 HD2 PRO A 14 33.564 -3.425 14.021 1.00 0.00 H +ATOM 205 HD3 PRO A 14 33.775 -1.449 14.137 1.00 0.00 H +ATOM 206 OXT PRO A 14 29.767 -2.895 12.875 1.00 0.00 O +TER 207 PRO A 14 +END diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/2mlt_frag1/crystal_structure-openmmawsem.pdb b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/2mlt_frag1/crystal_structure-openmmawsem.pdb new file mode 100644 index 00000000..8e33286a --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/2mlt_frag1/crystal_structure-openmmawsem.pdb @@ -0,0 +1,79 @@ +ATOM 1 CA IGL A 1 43.603 -11.488 24.325 1.00 0.00 C +ATOM 2 C IGL A 1 43.264 -10.199 23.553 1.00 0.00 C +ATOM 3 O IGL A 1 42.111 -9.896 23.277 1.00 0.00 O +ATOM 4 N NGP A 2 44.302 -9.461 23.220 1.00 0.00 N +ATOM 5 H NGP A 2 45.234 -9.706 23.444 1.00 0.00 H +ATOM 6 CA NGP A 2 44.200 -8.183 22.475 1.00 0.00 C +ATOM 7 C NGP A 2 43.789 -8.583 21.072 1.00 0.00 C +ATOM 8 O NGP A 2 43.068 -7.904 20.409 1.00 0.00 O +ATOM 9 CB NGP A 2 45.525 -7.320 22.425 1.00 0.00 B +ATOM 10 N IGL A 3 44.271 -9.699 20.648 1.00 0.00 N +ATOM 11 H IGL A 3 44.854 -10.247 21.184 1.00 0.00 H +ATOM 12 CA IGL A 3 43.999 -10.264 19.329 1.00 0.00 C +ATOM 13 C IGL A 3 42.477 -10.433 19.116 1.00 0.00 C +ATOM 14 O IGL A 3 41.912 -10.061 18.096 1.00 0.00 O +ATOM 15 N NGP A 4 41.843 -11.003 20.106 1.00 0.00 N +ATOM 16 H NGP A 4 42.300 -11.303 20.929 1.00 0.00 H +ATOM 17 CA NGP A 4 40.378 -11.260 20.106 1.00 0.00 C +ATOM 18 C NGP A 4 39.591 -9.927 20.070 1.00 0.00 C +ATOM 19 O NGP A 4 38.676 -9.747 19.278 1.00 0.00 O +ATOM 20 CB NGP A 4 40.061 -12.080 21.350 1.00 0.00 B +ATOM 21 N NGP A 5 39.977 -9.009 20.948 1.00 0.00 N +ATOM 22 H NGP A 5 40.716 -9.155 21.587 1.00 0.00 H +ATOM 23 CA NGP A 5 39.355 -7.658 21.083 1.00 0.00 C +ATOM 24 C NGP A 5 39.522 -6.938 19.719 1.00 0.00 C +ATOM 25 O NGP A 5 38.626 -6.314 19.126 1.00 0.00 O +ATOM 26 CB NGP A 5 39.843 -6.933 22.338 1.00 0.00 B +ATOM 27 N NGP A 6 40.693 -7.047 19.250 1.00 0.00 N +ATOM 28 H NGP A 6 41.417 -7.550 19.729 1.00 0.00 H +ATOM 29 CA NGP A 6 41.062 -6.432 17.957 1.00 0.00 C +ATOM 30 C NGP A 6 40.142 -6.853 16.792 1.00 0.00 C +ATOM 31 O NGP A 6 39.649 -6.121 16.029 1.00 0.00 O +ATOM 32 CB NGP A 6 42.627 -6.461 17.880 1.00 0.00 B +ATOM 33 N NGP A 7 39.932 -8.047 16.685 1.00 0.00 N +ATOM 34 H NGP A 7 40.331 -8.638 17.301 1.00 0.00 H +ATOM 35 CA NGP A 7 39.079 -8.646 15.636 1.00 0.00 C +ATOM 36 C NGP A 7 37.648 -8.086 15.716 1.00 0.00 C +ATOM 37 O NGP A 7 37.031 -7.839 14.731 1.00 0.00 O +ATOM 38 CB NGP A 7 38.854 -10.176 15.616 1.00 0.00 B +ATOM 39 N NGP A 8 37.150 -7.899 16.913 1.00 0.00 N +ATOM 40 H NGP A 8 37.650 -8.099 17.708 1.00 0.00 H +ATOM 41 CA NGP A 8 35.792 -7.369 17.211 1.00 0.00 C +ATOM 42 C NGP A 8 35.726 -5.888 16.790 1.00 0.00 C +ATOM 43 O NGP A 8 34.775 -5.402 16.257 1.00 0.00 O +ATOM 44 CB NGP A 8 35.113 -7.600 18.562 1.00 0.00 B +ATOM 45 N NGP A 9 36.761 -5.197 17.048 1.00 0.00 N +ATOM 46 H NGP A 9 37.529 -5.589 17.478 1.00 0.00 H +ATOM 47 CA NGP A 9 36.899 -3.759 16.725 1.00 0.00 C +ATOM 48 C NGP A 9 36.819 -3.547 15.216 1.00 0.00 C +ATOM 49 O NGP A 9 36.328 -2.551 14.694 1.00 0.00 O +ATOM 50 CB NGP A 9 38.227 -3.088 17.147 1.00 0.00 B +ATOM 51 N NGP A 10 37.315 -4.511 14.543 1.00 0.00 N +ATOM 52 H NGP A 10 37.713 -5.315 14.965 1.00 0.00 H +ATOM 53 CA NGP A 10 37.338 -4.508 13.084 1.00 0.00 C +ATOM 54 C NGP A 10 36.056 -4.969 12.347 1.00 0.00 C +ATOM 55 O NGP A 10 35.694 -4.554 11.333 1.00 0.00 O +ATOM 56 CB NGP A 10 38.687 -5.179 12.486 1.00 0.00 B +ATOM 57 N NGP A 11 35.391 -5.834 12.890 1.00 0.00 N +ATOM 58 H NGP A 11 35.684 -6.169 13.708 1.00 0.00 H +ATOM 59 CA NGP A 11 34.132 -6.405 12.343 1.00 0.00 C +ATOM 60 C NGP A 11 32.791 -6.284 13.093 1.00 0.00 C +ATOM 61 O NGP A 11 31.823 -5.889 12.630 1.00 0.00 O +ATOM 62 CB NGP A 11 34.462 -7.925 11.935 1.00 0.00 B +ATOM 63 N IGL A 12 32.772 -6.635 14.257 1.00 0.00 N +ATOM 64 H IGL A 12 33.554 -6.954 14.631 1.00 0.00 H +ATOM 65 CA IGL A 12 31.584 -6.595 15.140 1.00 0.00 C +ATOM 66 C IGL A 12 31.174 -5.191 15.577 1.00 0.00 C +ATOM 67 O IGL A 12 30.060 -4.914 15.603 1.00 0.00 O +ATOM 68 N NGP A 13 32.107 -4.323 15.915 1.00 0.00 N +ATOM 69 H NGP A 13 33.007 -4.547 15.894 1.00 0.00 H +ATOM 70 CA NGP A 13 31.923 -2.919 16.364 1.00 0.00 C +ATOM 71 C NGP A 13 31.169 -2.016 15.360 1.00 0.00 C +ATOM 72 O NGP A 13 30.232 -1.308 15.679 1.00 0.00 O +ATOM 73 CB NGP A 13 33.146 -2.183 17.008 1.00 0.00 B +ATOM 74 N IPR A 14 31.608 -2.065 14.147 1.00 0.00 N +ATOM 75 CA IPR A 14 31.026 -1.278 13.030 1.00 0.00 C +ATOM 76 O IPR A 14 28.657 -0.801 12.744 1.00 0.00 O +ATOM 77 CB IPR A 14 31.845 -1.614 11.816 1.00 0.00 B +TER 78 CB IPR A 14 +END diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/2mlt_frag1/crystal_structure.fasta b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/2mlt_frag1/crystal_structure.fasta new file mode 100644 index 00000000..32c6f937 --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/2mlt_frag1/crystal_structure.fasta @@ -0,0 +1,2 @@ +>CRYSTAL_STRUCTURE:A +GIGAVLKVLTTGLP diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/2mlt_frag1/crystal_structure.pdb b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/2mlt_frag1/crystal_structure.pdb new file mode 100644 index 00000000..4f7baad3 --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/2mlt_frag1/crystal_structure.pdb @@ -0,0 +1,210 @@ +REMARK 1 CREATED WITH OPENMM 8.1.1, 2025-12-23 +CRYST1 60.832 38.293 42.211 90.00 90.00 90.00 P 1 1 +ATOM 1 N GLY A 1 42.375 -12.180 24.780 1.00 0.00 N +ATOM 2 H GLY A 1 41.348 -11.623 25.042 1.00 0.00 H +ATOM 3 H2 GLY A 1 42.555 -12.690 25.854 1.00 0.00 H +ATOM 4 H3 GLY A 1 42.134 -13.162 24.137 1.00 0.00 H +ATOM 5 CA GLY A 1 43.603 -11.488 24.325 1.00 0.00 C +ATOM 6 HA2 GLY A 1 44.221 -11.213 25.312 1.00 0.00 H +ATOM 7 HA3 GLY A 1 44.301 -12.238 23.709 1.00 0.00 H +ATOM 8 C GLY A 1 43.288 -10.171 23.615 1.00 0.00 C +ATOM 9 O GLY A 1 42.111 -9.896 23.277 1.00 0.00 O +ATOM 10 N ILE A 2 44.323 -9.391 23.299 1.00 0.00 N +ATOM 11 H ILE A 2 45.380 -9.782 23.682 1.00 0.00 H +ATOM 12 CA ILE A 2 44.200 -8.183 22.475 1.00 0.00 C +ATOM 13 HA ILE A 2 43.338 -7.478 22.886 1.00 0.00 H +ATOM 14 C ILE A 2 43.750 -8.629 21.119 1.00 0.00 C +ATOM 15 O ILE A 2 43.068 -7.904 20.409 1.00 0.00 O +ATOM 16 CB ILE A 2 45.525 -7.320 22.425 1.00 0.00 C +ATOM 17 HB ILE A 2 46.450 -7.997 22.088 1.00 0.00 H +ATOM 18 CG1 ILE A 2 45.924 -6.837 23.820 1.00 0.00 C +ATOM 19 HG12 ILE A 2 46.792 -6.010 23.800 1.00 0.00 H +ATOM 20 HG13 ILE A 2 46.531 -7.674 24.425 1.00 0.00 H +ATOM 21 CG2 ILE A 2 45.555 -6.173 21.386 1.00 0.00 C +ATOM 22 HG21 ILE A 2 44.588 -5.494 21.214 1.00 0.00 H +ATOM 23 HG22 ILE A 2 46.339 -5.297 21.634 1.00 0.00 H +ATOM 24 HG23 ILE A 2 46.069 -6.532 20.365 1.00 0.00 H +ATOM 25 CD1 ILE A 2 44.837 -6.338 24.762 1.00 0.00 C +ATOM 26 HD11 ILE A 2 45.139 -5.222 25.094 1.00 0.00 H +ATOM 27 HD12 ILE A 2 44.872 -6.908 25.818 1.00 0.00 H +ATOM 28 HD13 ILE A 2 43.661 -6.128 24.665 1.00 0.00 H +ATOM 29 N GLY A 3 44.161 -9.867 20.749 1.00 0.00 N +ATOM 30 H GLY A 3 45.133 -10.465 21.085 1.00 0.00 H +ATOM 31 CA GLY A 3 43.999 -10.264 19.329 1.00 0.00 C +ATOM 32 HA2 GLY A 3 44.702 -9.646 18.587 1.00 0.00 H +ATOM 33 HA3 GLY A 3 44.390 -11.358 19.035 1.00 0.00 H +ATOM 34 C GLY A 3 42.433 -10.405 19.166 1.00 0.00 C +ATOM 35 O GLY A 3 41.912 -10.061 18.096 1.00 0.00 O +ATOM 36 N ALA A 4 41.862 -10.961 20.191 1.00 0.00 N +ATOM 37 H ALA A 4 42.465 -11.922 20.552 1.00 0.00 H +ATOM 38 CA ALA A 4 40.378 -11.260 20.106 1.00 0.00 C +ATOM 39 HA ALA A 4 40.148 -11.961 19.170 1.00 0.00 H +ATOM 40 C ALA A 4 39.584 -9.950 20.087 1.00 0.00 C +ATOM 41 O ALA A 4 38.676 -9.747 19.278 1.00 0.00 O +ATOM 42 CB ALA A 4 40.061 -12.080 21.350 1.00 0.00 C +ATOM 43 HB1 ALA A 4 39.843 -11.708 22.467 1.00 0.00 H +ATOM 44 HB2 ALA A 4 40.636 -13.124 21.485 1.00 0.00 H +ATOM 45 HB3 ALA A 4 38.960 -12.518 21.142 1.00 0.00 H +ATOM 46 N VAL A 5 39.936 -9.001 20.956 1.00 0.00 N +ATOM 47 H VAL A 5 40.629 -9.354 21.844 1.00 0.00 H +ATOM 48 CA VAL A 5 39.355 -7.658 21.083 1.00 0.00 C +ATOM 49 HA VAL A 5 38.259 -7.965 21.431 1.00 0.00 H +ATOM 50 C VAL A 5 39.536 -6.896 19.795 1.00 0.00 C +ATOM 51 O VAL A 5 38.626 -6.314 19.126 1.00 0.00 O +ATOM 52 CB VAL A 5 39.843 -6.933 22.338 1.00 0.00 C +ATOM 53 HB VAL A 5 40.988 -6.605 22.371 1.00 0.00 H +ATOM 54 CG1 VAL A 5 39.237 -5.519 22.413 1.00 0.00 C +ATOM 55 HG11 VAL A 5 38.051 -5.502 22.584 1.00 0.00 H +ATOM 56 HG12 VAL A 5 39.563 -4.681 21.625 1.00 0.00 H +ATOM 57 HG13 VAL A 5 39.559 -4.865 23.372 1.00 0.00 H +ATOM 58 CG2 VAL A 5 39.745 -7.587 23.653 1.00 0.00 C +ATOM 59 HG21 VAL A 5 39.713 -6.840 24.597 1.00 0.00 H +ATOM 60 HG22 VAL A 5 38.700 -8.144 23.855 1.00 0.00 H +ATOM 61 HG23 VAL A 5 40.504 -8.343 24.190 1.00 0.00 H +ATOM 62 N LEU A 6 40.752 -7.021 19.222 1.00 0.00 N +ATOM 63 H LEU A 6 41.432 -6.456 20.018 1.00 0.00 H +ATOM 64 CA LEU A 6 41.062 -6.432 17.957 1.00 0.00 C +ATOM 65 HA LEU A 6 40.866 -5.262 18.044 1.00 0.00 H +ATOM 66 C LEU A 6 40.230 -6.935 16.870 1.00 0.00 C +ATOM 67 O LEU A 6 39.649 -6.121 16.029 1.00 0.00 O +ATOM 68 CB LEU A 6 42.627 -6.461 17.880 1.00 0.00 C +ATOM 69 HB2 LEU A 6 43.172 -5.759 18.678 1.00 0.00 H +ATOM 70 HB3 LEU A 6 42.971 -7.600 17.910 1.00 0.00 H +ATOM 71 CG LEU A 6 43.125 -6.023 16.524 1.00 0.00 C +ATOM 72 HG LEU A 6 42.903 -6.713 15.576 1.00 0.00 H +ATOM 73 CD1 LEU A 6 42.706 -4.584 16.210 1.00 0.00 C +ATOM 74 HD11 LEU A 6 43.272 -4.298 15.188 1.00 0.00 H +ATOM 75 HD12 LEU A 6 43.196 -3.769 16.945 1.00 0.00 H +ATOM 76 HD13 LEU A 6 41.687 -4.015 15.951 1.00 0.00 H +ATOM 77 CD2 LEU A 6 44.669 -6.152 16.638 1.00 0.00 C +ATOM 78 HD21 LEU A 6 45.189 -5.937 15.574 1.00 0.00 H +ATOM 79 HD22 LEU A 6 45.323 -5.404 17.311 1.00 0.00 H +ATOM 80 HD23 LEU A 6 45.194 -7.216 16.816 1.00 0.00 H +ATOM 81 N LYS A 7 39.981 -8.229 16.721 1.00 0.00 N +ATOM 82 H LYS A 7 40.772 -9.075 16.935 1.00 0.00 H +ATOM 83 CA LYS A 7 39.079 -8.646 15.636 1.00 0.00 C +ATOM 84 HA LYS A 7 39.583 -8.378 14.590 1.00 0.00 H +ATOM 85 C LYS A 7 37.648 -8.063 15.784 1.00 0.00 C +ATOM 86 O LYS A 7 37.031 -7.839 14.731 1.00 0.00 O +ATOM 87 CB LYS A 7 38.854 -10.176 15.616 1.00 0.00 C +ATOM 88 HB2 LYS A 7 37.977 -10.374 14.825 1.00 0.00 H +ATOM 89 HB3 LYS A 7 38.398 -10.663 16.606 1.00 0.00 H +ATOM 90 CG LYS A 7 40.011 -10.993 15.144 1.00 0.00 C +ATOM 91 HG2 LYS A 7 41.158 -10.886 15.464 1.00 0.00 H +ATOM 92 HG3 LYS A 7 40.110 -10.782 13.968 1.00 0.00 H +ATOM 93 CD LYS A 7 39.691 -12.487 15.325 1.00 0.00 C +ATOM 94 HD2 LYS A 7 39.801 -12.898 16.441 1.00 0.00 H +ATOM 95 HD3 LYS A 7 38.586 -12.748 14.951 1.00 0.00 H +ATOM 96 CE LYS A 7 40.599 -13.394 14.493 1.00 0.00 C +ATOM 97 HE2 LYS A 7 41.676 -13.535 14.991 1.00 0.00 H +ATOM 98 HE3 LYS A 7 40.872 -13.049 13.380 1.00 0.00 H +ATOM 99 NZ LYS A 7 39.966 -14.755 14.319 1.00 0.00 N +ATOM 100 HZ1 LYS A 7 39.465 -14.898 13.239 1.00 0.00 H +ATOM 101 HZ2 LYS A 7 40.794 -15.623 14.363 1.00 0.00 H +ATOM 102 HZ3 LYS A 7 39.153 -15.222 15.066 1.00 0.00 H +ATOM 103 N VAL A 8 37.111 -7.988 16.981 1.00 0.00 N +ATOM 104 H VAL A 8 37.403 -8.767 17.821 1.00 0.00 H +ATOM 105 CA VAL A 8 35.792 -7.369 17.211 1.00 0.00 C +ATOM 106 HA VAL A 8 35.091 -8.010 16.491 1.00 0.00 H +ATOM 107 C VAL A 8 35.776 -5.881 16.885 1.00 0.00 C +ATOM 108 O VAL A 8 34.775 -5.402 16.257 1.00 0.00 O +ATOM 109 CB VAL A 8 35.113 -7.600 18.562 1.00 0.00 C +ATOM 110 HB VAL A 8 34.034 -7.086 18.529 1.00 0.00 H +ATOM 111 CG1 VAL A 8 34.774 -9.045 18.851 1.00 0.00 C +ATOM 112 HG11 VAL A 8 33.742 -9.377 18.329 1.00 0.00 H +ATOM 113 HG12 VAL A 8 34.457 -9.332 19.975 1.00 0.00 H +ATOM 114 HG13 VAL A 8 35.415 -10.026 18.593 1.00 0.00 H +ATOM 115 CG2 VAL A 8 35.769 -6.970 19.726 1.00 0.00 C +ATOM 116 HG21 VAL A 8 36.472 -7.757 20.279 1.00 0.00 H +ATOM 117 HG22 VAL A 8 36.066 -5.819 19.842 1.00 0.00 H +ATOM 118 HG23 VAL A 8 34.929 -6.899 20.590 1.00 0.00 H +ATOM 119 N LEU A 9 36.860 -5.176 17.216 1.00 0.00 N +ATOM 120 H LEU A 9 37.858 -5.414 17.783 1.00 0.00 H +ATOM 121 CA LEU A 9 36.899 -3.759 16.725 1.00 0.00 C +ATOM 122 HA LEU A 9 36.033 -3.017 17.052 1.00 0.00 H +ATOM 123 C LEU A 9 36.778 -3.644 15.254 1.00 0.00 C +ATOM 124 O LEU A 9 36.328 -2.551 14.694 1.00 0.00 O +ATOM 125 CB LEU A 9 38.227 -3.088 17.147 1.00 0.00 C +ATOM 126 HB2 LEU A 9 39.189 -3.378 16.504 1.00 0.00 H +ATOM 127 HB3 LEU A 9 38.137 -1.956 16.758 1.00 0.00 H +ATOM 128 CG LEU A 9 38.462 -3.091 18.615 1.00 0.00 C +ATOM 129 HG LEU A 9 38.754 -3.955 19.375 1.00 0.00 H +ATOM 130 CD1 LEU A 9 39.783 -2.288 18.873 1.00 0.00 C +ATOM 131 HD11 LEU A 9 40.856 -2.781 19.080 1.00 0.00 H +ATOM 132 HD12 LEU A 9 39.745 -1.582 19.847 1.00 0.00 H +ATOM 133 HD13 LEU A 9 40.098 -1.424 18.099 1.00 0.00 H +ATOM 134 CD2 LEU A 9 37.265 -2.535 19.351 1.00 0.00 C +ATOM 135 HD21 LEU A 9 37.115 -1.380 19.067 1.00 0.00 H +ATOM 136 HD22 LEU A 9 36.218 -3.088 19.520 1.00 0.00 H +ATOM 137 HD23 LEU A 9 37.478 -2.347 20.522 1.00 0.00 H +ATOM 138 N THR A 10 37.320 -4.627 14.530 1.00 0.00 N +ATOM 139 H THR A 10 37.840 -5.625 14.880 1.00 0.00 H +ATOM 140 CA THR A 10 37.338 -4.508 13.084 1.00 0.00 C +ATOM 141 HA THR A 10 37.440 -3.390 12.679 1.00 0.00 H +ATOM 142 C THR A 10 36.072 -5.022 12.458 1.00 0.00 C +ATOM 143 O THR A 10 35.694 -4.554 11.333 1.00 0.00 O +ATOM 144 CB THR A 10 38.687 -5.179 12.486 1.00 0.00 C +ATOM 145 HB THR A 10 38.867 -4.707 11.403 1.00 0.00 H +ATOM 146 OG1 THR A 10 38.285 -6.538 12.354 1.00 0.00 O +ATOM 147 HG1 THR A 10 39.022 -7.085 11.599 1.00 0.00 H +ATOM 148 CG2 THR A 10 39.877 -5.049 13.451 1.00 0.00 C +ATOM 149 HG21 THR A 10 40.525 -5.741 14.176 1.00 0.00 H +ATOM 150 HG22 THR A 10 40.717 -5.188 12.594 1.00 0.00 H +ATOM 151 HG23 THR A 10 40.027 -3.875 13.642 1.00 0.00 H +ATOM 152 N THR A 11 35.315 -5.870 13.113 1.00 0.00 N +ATOM 153 H THR A 11 35.402 -6.359 14.181 1.00 0.00 H +ATOM 154 CA THR A 11 34.132 -6.405 12.343 1.00 0.00 C +ATOM 155 HA THR A 11 33.776 -5.952 11.299 1.00 0.00 H +ATOM 156 C THR A 11 32.874 -6.299 13.140 1.00 0.00 C +ATOM 157 O THR A 11 31.823 -5.889 12.630 1.00 0.00 O +ATOM 158 CB THR A 11 34.462 -7.925 11.935 1.00 0.00 C +ATOM 159 HB THR A 11 33.509 -8.482 11.478 1.00 0.00 H +ATOM 160 OG1 THR A 11 34.702 -8.591 13.199 1.00 0.00 O +ATOM 161 HG1 THR A 11 34.748 -9.764 13.020 1.00 0.00 H +ATOM 162 CG2 THR A 11 35.695 -7.959 11.047 1.00 0.00 C +ATOM 163 HG21 THR A 11 35.174 -7.957 9.962 1.00 0.00 H +ATOM 164 HG22 THR A 11 36.601 -7.258 10.698 1.00 0.00 H +ATOM 165 HG23 THR A 11 36.212 -9.042 11.053 1.00 0.00 H +ATOM 166 N GLY A 12 32.918 -6.606 14.420 1.00 0.00 N +ATOM 167 H GLY A 12 33.201 -7.715 14.741 1.00 0.00 H +ATOM 168 CA GLY A 12 31.584 -6.595 15.140 1.00 0.00 C +ATOM 169 HA2 GLY A 12 31.429 -7.241 16.136 1.00 0.00 H +ATOM 170 HA3 GLY A 12 30.674 -7.036 14.498 1.00 0.00 H +ATOM 171 C GLY A 12 31.264 -5.168 15.584 1.00 0.00 C +ATOM 172 O GLY A 12 30.060 -4.914 15.603 1.00 0.00 O +ATOM 173 N LEU A 13 32.195 -4.276 15.948 1.00 0.00 N +ATOM 174 H LEU A 13 32.473 -4.884 16.934 1.00 0.00 H +ATOM 175 CA LEU A 13 31.923 -2.919 16.364 1.00 0.00 C +ATOM 176 HA LEU A 13 30.998 -3.094 17.098 1.00 0.00 H +ATOM 177 C LEU A 13 31.251 -2.004 15.324 1.00 0.00 C +ATOM 178 O LEU A 13 30.232 -1.308 15.679 1.00 0.00 O +ATOM 179 CB LEU A 13 33.146 -2.183 17.008 1.00 0.00 C +ATOM 180 HB2 LEU A 13 33.863 -3.073 17.325 1.00 0.00 H +ATOM 181 HB3 LEU A 13 33.501 -1.235 16.375 1.00 0.00 H +ATOM 182 CG LEU A 13 32.913 -1.523 18.351 1.00 0.00 C +ATOM 183 HG LEU A 13 32.879 -2.314 19.248 1.00 0.00 H +ATOM 184 CD1 LEU A 13 33.999 -0.517 18.760 1.00 0.00 C +ATOM 185 HD11 LEU A 13 34.965 -0.295 18.088 1.00 0.00 H +ATOM 186 HD12 LEU A 13 33.658 0.633 18.847 1.00 0.00 H +ATOM 187 HD13 LEU A 13 34.370 -0.681 19.889 1.00 0.00 H +ATOM 188 CD2 LEU A 13 31.587 -0.842 18.531 1.00 0.00 C +ATOM 189 HD21 LEU A 13 31.499 -0.196 19.543 1.00 0.00 H +ATOM 190 HD22 LEU A 13 31.256 0.004 17.748 1.00 0.00 H +ATOM 191 HD23 LEU A 13 30.609 -1.496 18.772 1.00 0.00 H +ATOM 192 N PRO A 14 31.689 -1.979 14.106 1.00 0.00 N +ATOM 193 CA PRO A 14 31.026 -1.278 13.030 1.00 0.00 C +ATOM 194 HA PRO A 14 30.971 -0.101 13.220 1.00 0.00 H +ATOM 195 C PRO A 14 29.521 -1.670 12.857 1.00 0.00 C +ATOM 196 O PRO A 14 28.657 -0.801 12.744 1.00 0.00 O +ATOM 197 CB PRO A 14 31.845 -1.614 11.816 1.00 0.00 C +ATOM 198 HB2 PRO A 14 31.257 -2.227 10.972 1.00 0.00 H +ATOM 199 HB3 PRO A 14 32.036 -0.613 11.183 1.00 0.00 H +ATOM 200 CG PRO A 14 33.118 -2.205 12.303 1.00 0.00 C +ATOM 201 HG2 PRO A 14 33.250 -3.166 11.606 1.00 0.00 H +ATOM 202 HG3 PRO A 14 34.010 -1.511 11.899 1.00 0.00 H +ATOM 203 CD PRO A 14 33.098 -2.363 13.769 1.00 0.00 C +ATOM 204 HD2 PRO A 14 33.564 -3.425 14.021 1.00 0.00 H +ATOM 205 HD3 PRO A 14 33.775 -1.449 14.137 1.00 0.00 H +ATOM 206 OXT PRO A 14 29.767 -2.895 12.875 1.00 0.00 O +TER 207 PRO A 14 +END diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/2mlt_frag1/forces_setup.py b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/2mlt_frag1/forces_setup.py new file mode 100644 index 00000000..49f5b654 --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/2mlt_frag1/forces_setup.py @@ -0,0 +1,46 @@ +from openawsem.functionTerms import * +from openawsem.helperFunctions.myFunctions import * + +try: + from openmm.unit import angstrom + from openmm.unit import kilocalorie_per_mole +except ModuleNotFoundError: + from simtk.unit import angstrom + from simtk.unit import kilocalorie_per_mole + +def set_up_forces(oa, computeQ=False, submode=-1, contactParameterLocation=".", membrane_center=-0*angstrom): + # apply forces + forces = [ + basicTerms.con_term(oa), + basicTerms.chain_term(oa), + basicTerms.chi_term(oa), + basicTerms.excl_term(oa), + basicTerms.rama_term(oa), + basicTerms.rama_proline_term(oa), + basicTerms.rama_ssweight_term(oa, k_rama_ssweight=2*8.368), + contactTerms.contact_term(oa), + # for membrane protein simulation use contact_term below. + # contact_term(oa, z_dependent=True, inMembrane=True, membrane_center=membrane_center, k_relative_mem=3), + hydrogenBondTerms.beta_term_1(oa), + hydrogenBondTerms.beta_term_2(oa), + hydrogenBondTerms.beta_term_3(oa), + hydrogenBondTerms.pap_term_1(oa), + hydrogenBondTerms.pap_term_2(oa), + # membraneTerms.membrane_term(oa, k=1*kilocalorie_per_mole, membrane_center=membrane_center), + # membraneTerms.membrane_preassigned_term(oa, k=1*kilocalorie_per_mole, membrane_center=membrane_center, zimFile="PredictedZim"), + # templateTerms.er_term(oa), + # templateTerms.fragment_memory_term(oa, frag_file_list_file="./frags.mem", npy_frag_table="./frags.npy", UseSavedFragTable=True), + templateTerms.fragment_memory_term(oa, frag_file_list_file="./single_frags.mem", npy_frag_table="./single_frags.npy", UseSavedFragTable=False), + debyeHuckelTerms.debye_huckel_term(oa, chargeFile="charge.txt"), + ] + if computeQ: + forces.append(biasTerms.rg_term(oa)) + forces.append(biasTerms.q_value(oa, "crystal_structure-cleaned.pdb", forceGroup=1)) + forces.append(biasTerms.qc_value(oa, "crystal_structure-cleaned.pdb")) + # forces.append(partial_q_value(oa, "crystal_structure-cleaned.pdb", residueIndexGroup=list(range(0, 15)), forceGroup=1)) + if submode == 0: + additional_forces = [ + # contact_term(oa), + ] + forces += additional_forces + return forces diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/2mlt_frag1/gamma.dat b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/2mlt_frag1/gamma.dat new file mode 100644 index 00000000..ebe8e61b --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/2mlt_frag1/gamma.dat @@ -0,0 +1,421 @@ + 0.72008 0.72008 +-0.27029 -0.27029 +-0.25968 -0.25968 +-0.40222 -0.40222 + 0.62053 0.62053 +-0.24469 -0.24469 +-0.34851 -0.34851 +-0.11391 -0.11391 +-0.12511 -0.12511 + 1.00000 1.00000 + 1.00000 1.00000 +-0.45156 -0.45156 + 0.50732 0.50732 + 0.56857 0.56857 +-0.53459 -0.53459 +-0.20625 -0.20625 + 0.08004 0.08004 + 0.39663 0.39663 + 0.11183 0.11183 + 0.91795 0.91795 +-0.64172 -0.64172 +-0.28113 -0.28113 + 0.40922 0.40922 +-0.40038 -0.40038 +-0.20918 -0.20918 +-0.03378 -0.03378 +-0.32864 -0.32864 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+from openawsem import * +from openawsem.helperFunctions.myFunctions import * + +def analyze(args): + if (args.debug): + do = print + cd = print + else: + do = os.system + cd = os.chdir + + # if mm_run.py is not at the same location of your setup folder. + setupFolderPath = os.path.dirname(args.protein) + setupFolderPath = "." if setupFolderPath == "" else setupFolderPath + proteinName = pdb_id = os.path.basename(args.protein) + chain=args.chain + pdb = f"{pdb_id}.pdb" + + trajectoryPath = os.path.abspath(args.trajectory) + if args.output is None: + outFile = os.path.join(os.path.dirname(trajectoryPath), "info.dat") + else: + outFile = os.path.join(os.path.dirname(trajectoryPath), args.output) + + forceSetupFile = None if args.forces is None else os.path.abspath(args.forces) + parametersLocation = "." if args.parameters is None else os.path.abspath(args.parameters) + os.chdir(setupFolderPath) + + simulation_platform = args.platform + platform = Platform.getPlatformByName(simulation_platform) + if simulation_platform == "CPU": + if args.thread != -1: + platform.setPropertyDefaultValue("Threads", str(args.thread)) + print(f"{simulation_platform}: {platform.getPropertyDefaultValue('Threads')} threads") + + + + if chain == "-1": + chain = getAllChains("crystal_structure.pdb") + print("Chains to simulate: ", chain) + + # for compute Q + if args.fromOpenMMPDB: + input_pdb_filename = proteinName + seq=read_fasta("crystal_structure.fasta") + print(f"Using Seq:\n{seq}") + else: + suffix = '-openmmawsem.pdb' + if pdb_id[-len(suffix):] == suffix: + input_pdb_filename = pdb_id + else: + input_pdb_filename = f"{pdb_id}-openmmawsem.pdb" + seq=None + + if args.fasta == "": + seq = None + else: + seq = seq=read_fasta(args.fasta) + print(f"Using Seq:\n{seq}") + + fileType = trajectoryPath[-3:] + if fileType == "pdb": + pdb_trajectory = md.load(trajectoryPath, stride=1) + elif fileType == "dcd": + pdb_trajectory = md.load(trajectoryPath, top=input_pdb_filename, stride=1) + # may use iterload if loading still too slow + else: + print(f"Unknown fileType {fileType}") + # pdb_trajectory = read_trajectory_pdb_positions(trajectoryPath) + + # check for atoms whose positions are intended to be fixed + if args.fixed_residue_indices: + with open(args.fixed_residue_indices,'r') as f: + for line in f: # only expect 1 line + fixed_residue_indices = line.strip().split(',') #expecting a one-line csv + fixed_residue_indices = [int(item) for item in fixed_residue_indices] + break + else: + fixed_residue_indices = [] + + oa = OpenMMAWSEMSystem(input_pdb_filename, chains=chain, k_awsem=1.0, xml_filename=openawsem.xml, seqFromPdb=seq, + fixed_residue_indices=fixed_residue_indices,periodic_box=args.periodic_box, + includeLigands=args.includeLigands) # k_awsem is an overall scaling factor that will affect the relevant temperature scales + + print(f"using force setup file from {forceSetupFile}") + spec = importlib.util.spec_from_file_location("forces", forceSetupFile) + # print(spec) + forces = importlib.util.module_from_spec(spec) + spec.loader.exec_module(forces) + forces = forces.set_up_forces(oa, computeQ=True, submode=args.subMode, contactParameterLocation=parametersLocation) + oa.addForcesWithDefaultForceGroup(forces) + # print(forces) + + # start simulation + collision_rate = 5.0 / picoseconds + + integrator = LangevinIntegrator(300*kelvin, 1/picosecond, 2*femtoseconds) + simulation = Simulation(oa.pdb.topology, oa.system, integrator, platform) + + # apply forces + forceGroupTable = {"Backbone":20, "Rama":21, "Contact":22, "Fragment":23, "Membrane":24, "ER":25, "TBM_Q":26, "Beta":27, "Pap":28, "Helical":29, + "Q":1, "Rg":2, "Qc":3, + "Helix_orientation":18, "Pulling":19, "Debye_huckel":30, + "Total":list(range(11, 32)) + # , "Q_wat":4, "Q_mem":5, + } + print("Please ensure the forceGroupTable in mm_analysis is set up correctly if you are adding new energy terms.") + print("Also, please notice that the total energy include all the terms with group index range from 11 to 32.") + # forceGroupTable = {"Con":11, "Chain":12, "Chi":13, "Excluded":14, "Rama":15, "Direct":16, + # "Burial":17, "Mediated":18, "Contact":18, "Fragment":19, "Membrane":20, "ER":21,"TBM_Q":22, "beta_1":23, "beta_2":24,"beta_3":25,"pap":26, "Total":list(range(11, 32)), + # "Water":[16, 18], "Beta":[23, 24, 25], "Pap":26, "Rg_Bias":27, "Helical":28, "Pulling":29, "Q":1, "Rg":2, "Qc":3, "Q_wat":4, "Q_mem":5} + # forceGroupTable_Rev = {11:"Con", 12:"Chain", 13:"Chi", 14:"Excluded", 15:"Rama", 16:"Direct", + # 17:"Burial", 18:"Mediated", 19:"Fragment"} + # forceGroupTable = {"Con":11, "Chain":12, "Chi":13, "Excluded":14, "Rama":15, "Direct":16, + # "Burial":17, "Mediated":18, "Contact":18, "Fragment":19, "Membrane":20, "ER":21,"TBM_Q":22, "beta_1":23, "beta_2":24,"beta_3":25,"pap":26, "Total":list(range(11, 27)), + # "Water":[16, 18], "Beta":[23, 24, 25], "Pap":26, "Q":1} + # forceGroupTable = {"Con":11, "Chain":12, "Chi":13, "Excluded":14, "Rama":15, "Direct":16, + # "Burial":17, "Mediated":18, "Contact":18, "Fragment":19, "Membrane":20, "ER":21,"TBM_Q":22, "beta_1":23, "Total":list(range(11, 26)), + # "Water":[16, 18], "beta":[23, 24, 25], "Q":1} + showValue = ["Q", "Qc", "Rg"] + # term in showEnergy will assume to take on the energy unit of kilojoule_per_mole, it will be shown in unit of kilocalories_per_mole(divided by 4.184) + # term in showValue will not be converted. + showEnergy = ["Backbone", "Rama", "Contact", "Fragment", "Membrane", "ER", "TBM_Q", "Beta", "Pap", "Helical", "Debye_huckel","Total"] + showAll = showValue + showEnergy + # , "Disulfide" + # showEnergy = ["Q", "Qc", "Rg", "Con", "Chain", "Chi", "Excluded", "Rama", "Contact", "Helical", "Fragment", "Membrane", "ER", "Beta", "Pap", "Total"] + # showEnergy = ["Q", "Qc", "Rg", "Pulling", "Con", "Chain", "Chi", "Excluded", "Rama", "Contact", "FamilyFold", "Fragment", "Membrane", "Beta", "Pap", "Rg_Bias", "Total"] + # showEnergy = ["Q", "Con", "Chain", "Chi", "Excluded", "Rama", "Contact", "Fragment", "Membrane", "Beta", "Pap", "Total"] + # showEnergy = ["Q", "Con", "Chain", "Chi", "Excluded", "Rama", "Contact", "Fragment", "Membrane", "Total"] + # showEnergy = ["Q", "Con", "Chain", "Chi", "Excluded", "Rama", "Contact", "Fragment", "Membrane","ER","TBM_Q","beta_1", "Total"] + # showEnergy = ["Q", "Con", "Chain", "Chi", "Excluded", "Rama", "Contact", "Fragment", "Membrane","ER","TBM_Q","beta_1","beta_2","beta_3","pap", "Total"] + # print("Steps", *showEnergy) + print("Printing energies") + + with open(outFile, "w") as out: + line = " ".join(["{0:<8s}".format(i) for i in ["Steps"] + showAll]) + print(line) + out.write(line+"\n") + # for step, pdb in enumerate(pdb_trajectory): + # simulation.context.setPositions(pdb.positions) + for step in range(len(pdb_trajectory)): + simulation.context.setPositions(pdb_trajectory.openmm_positions(step)) + e = [] + for term in showAll: + if type(forceGroupTable[term]) == list: + g = set(forceGroupTable[term]) + elif forceGroupTable[term] == -1: + g = -1 + else: + g = {forceGroupTable[term]} + state = simulation.context.getState(getEnergy=True, groups=g) + # if term == "Q" or term == "Rg" or term == "Qc" or term == "Q_wat" or term == "Q_mem": + if term in showValue: + termEnergy = state.getPotentialEnergy().value_in_unit(kilojoule_per_mole) + else: + termEnergy = state.getPotentialEnergy().value_in_unit(kilocalories_per_mole) + e.append(termEnergy) + # print(*e) + line = " ".join([f"{step:<8}"] + ["{0:<8.2f}".format(i) for i in e]) + print(line) + out.write(line+"\n") + # print(forceGroupTable[term], state.getPotentialEnergy().value_in_unit(kilocalories_per_mole)) + +def main(args=None): + parser = argparse.ArgumentParser( + description="The goal of this python3 code is to automatically create \ + the project template as fast as possible. Written by Wei Lu." + ) + parser.add_argument("protein", help="The name of the protein") + parser.add_argument("-d", "--debug", action="store_true", default=False) + parser.add_argument("-c", "--chain", type=str, default="-1") + parser.add_argument("--thread", type=int, default=2, help="default is using 2 CPUs, -1 is using all") + parser.add_argument("-p", "--platform", type=str, default="CPU", help="Could be OpenCL, CUDA and CPU") + parser.add_argument("-t", "--trajectory", type=str, default="./movie.pdb") + parser.add_argument("-o", "--output", type=str, default=None, help="The Name of file that shows your energy and Q information.") + parser.add_argument("--subMode", type=int, default=3) + parser.add_argument("-f", "--forces", default="forces_setup.py") + parser.add_argument("--parameters", default=None) + parser.add_argument("--fromOpenMMPDB", action="store_true", default=False) + parser.add_argument("--fasta", type=str, default="crystal_structure.fasta") + parser.add_argument("--includeLigands", action="store_true", default=False) + parser.add_argument('--periodic_box', type=float, nargs=3, metavar=('X', 'Y', 'Z'), help='Enable periodic boundary conditions with box dimensions in x, y, z (nanometers)') + parser.add_argument('--fixed_residue_indices', type=str, default='', help='csv file with indices (not "ids" or "resnums") of residues whose positions should be fixed)') + + if args is None: + args = parser.parse_args() + else: + args = parser.parse_args(args) + + with open('analysis_commandline_args.txt', 'a') as f: + f.write(' '.join(sys.argv)) + f.write('\n') + print(' '.join(sys.argv)) + analyze(args) + +if __name__=="__main__": + main() diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/2mlt_frag1/mm_run.py b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/2mlt_frag1/mm_run.py new file mode 100755 index 00000000..ad3064b4 --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/2mlt_frag1/mm_run.py @@ -0,0 +1,377 @@ +#!/usr/bin/env python3 +import os +import sys +import time +import argparse +import importlib.util + +from openawsem import * +from openawsem.helperFunctions.myFunctions import * + +do = os.system +cd = os.chdir + +def run(args): + simulation_platform = args.platform + platform = Platform.getPlatformByName(simulation_platform) + if simulation_platform == "CPU": + if args.thread != -1: + platform.setPropertyDefaultValue("Threads", str(args.thread)) + print(f"{simulation_platform}: {platform.getPropertyDefaultValue('Threads')} threads") + elif simulation_platform=="OpenCL": + platform.setPropertyDefaultValue('OpenCLPlatformIndex', '0') + platform.setPropertyDefaultValue('DeviceIndex', str(args.device)) + elif simulation_platform=="CUDA": + platform.setPropertyDefaultValue('DeviceIndex', str(args.device)) + + # if mm_run.py is not at the same location of your setup folder. + setupFolderPath = os.path.dirname(args.protein) + setupFolderPath = "." if setupFolderPath == "" else setupFolderPath + proteinName = pdb_id = os.path.basename(args.protein) + + pwd = os.getcwd() + toPath = os.path.abspath(args.to) + checkPointPath = None if args.fromCheckPoint is None else os.path.abspath(args.fromCheckPoint) + forceSetupFile = None if args.forces is None else os.path.abspath(args.forces) + parametersLocation = "." if args.parameters is None else os.path.abspath(args.parameters) + os.chdir(setupFolderPath) + + + + # chain=args.chain + chain=args.chain + pdb = f"{pdb_id}.pdb" + + if chain == "-1": + chain = getAllChains("crystal_structure.pdb") + print("Chains to simulate: ", chain) + + + if args.to != "./": + # os.system(f"mkdir -p {args.to}") + os.makedirs(toPath, exist_ok=True) + os.system(f"cp {forceSetupFile} {toPath}/forces_setup.py") + os.system(f"cp crystal_structure.fasta {toPath}/") + os.system(f"cp crystal_structure.pdb {toPath}/") + # os.system(f"cp {pdb} {args.to}/{pdb}") + # pdb = os.path.join(args.to, pdb) + + if args.fromOpenMMPDB: + input_pdb_filename = proteinName + seq=read_fasta("crystal_structure.fasta") + print(f"Using Seq:\n{seq}") + else: + suffix = '-openmmawsem.pdb' + if pdb_id[-len(suffix):] == suffix: + input_pdb_filename = pdb_id + else: + input_pdb_filename = f"{pdb_id}-openmmawsem.pdb" + seq=None + + if args.fasta == "": + seq = None + else: + seq = seq=read_fasta(args.fasta) + print(f"Using Seq:\n{seq}") + # start simulation + collision_rate = 5.0 / picoseconds + + # check for atoms whose positions are intended to be fixed + if args.fixed_residue_indices: + with open(args.fixed_residue_indices,'r') as f: + for line in f: # only expect 1 line + fixed_residue_indices = line.strip().split(',') #expecting a one-line csv + fixed_residue_indices = [int(item) for item in fixed_residue_indices] + break + else: + fixed_residue_indices = [] + + # assign annealing parameters + Tstart = args.tempStart + Tend = args.tempEnd + + print(f"using force setup file from {forceSetupFile}") + spec = importlib.util.spec_from_file_location("forces", forceSetupFile) + # print(spec) + forces = importlib.util.module_from_spec(spec) + spec.loader.exec_module(forces) + + + oa = OpenMMAWSEMSystem(input_pdb_filename, k_awsem=1.0, chains=chain, xml_filename=openawsem.xml, seqFromPdb=seq, + includeLigands=args.includeLigands, periodic_box=args.periodic_box, + fixed_residue_indices=fixed_residue_indices) # k_awsem is an overall scaling factor that will affect the relevant temperature scales + myForces = forces.set_up_forces(oa, submode=args.subMode, contactParameterLocation=parametersLocation,) + # print(forces) + # oa.addForces(myForces) + + if args.removeCMMotionRemover: + oa.system.removeForce(0) + oa.addForcesWithDefaultForceGroup(myForces) + + #Define output paths + output_path = os.path.join(toPath, "output.log") + native_pdb_path = os.path.join(toPath, "native.pdb") + movie_pdb_path = os.path.join(toPath, "movie.pdb") + movie_dcd_path = os.path.join(toPath, "movie.dcd") + time_dat_path = os.path.join(toPath, "time.dat") + info_dat_path = os.path.join(toPath, "info.dat") + checkpoint_path = os.path.join(toPath, args.checkpointFile) + + if args.fromCheckPoint: + integrator = LangevinIntegrator(Tstart*kelvin, 1/picosecond, args.timeStep*femtoseconds) + simulation = Simulation(oa.pdb.topology, oa.system, integrator, platform) + simulation.loadCheckpoint(checkPointPath) + reporter_append = True + else: + # output the native and the structure after minimization + integrator = CustomIntegrator(0.001) + simulation = Simulation(oa.pdb.topology, oa.system, integrator, platform) + simulation.context.setPositions(oa.pdb.positions) # set the initial positions of the atoms + + simulation.reporters.append(PDBReporter(native_pdb_path, 1)) + simulation.reporters.append(DCDReporter(movie_dcd_path, 1)) + + simulation.step(int(1)) + simulation.minimizeEnergy() # first, minimize the energy to a local minimum to reduce any large forces that might be present + simulation.step(int(1)) + reporter_append = False + + + # print("------------------Folding-------------------") + # oa = OpenMMAWSEMSystem(input_pdb_filename, k_awsem=1.0, chains=chain, xml_filename=OPENAWSEM_LOCATION+"awsem.xml") # k_awsem is an overall scaling factor that will affect the relevant temperature scales + # myForces = forces.set_up_forces(oa, submode=args.subMode, contactParameterLocation=parametersLocation) + # oa.addForces(myForces) + + integrator = LangevinIntegrator(Tstart*kelvin, 1/picosecond, args.timeStep*femtoseconds) + # integrator.setRandomNumberSeed(A_NUMBER_AS_RANDOM_SEED) + # integrator = CustomIntegrator(0.001) + simulation = Simulation(oa.pdb.topology, oa.system, integrator, platform) + # simulation.loadState(os.path.join(toPath, 'output.xml')) + simulation.context.setPositions(oa.pdb.positions) # set the initial positions of the atoms + simulation.context.setVelocitiesToTemperature(Tstart*kelvin) # set the initial velocities of the atoms according to the desired starting temperature + # simulation.context.setVelocitiesToTemperature(Tstart*kelvin, A_RANDOM_SEED_NUMBER) + simulation.minimizeEnergy() # first, minimize the energy to a local minimum to reduce any large forces that might be present + + + print("report_interval", args.reportInterval) + print("num_frames", args.numFrames) + + # Backup existing files + if reporter_append: + # Only backup checkpoint if it exists + if os.path.exists(checkpoint_path): + past_chk_dir = os.path.join(toPath, "past_checkpoints") + os.makedirs(past_chk_dir, exist_ok=True) + backup_counter = 0 + for i in range(1000): + backup_chk = os.path.join(past_chk_dir, f"checkpoint_used_{backup_counter:03d}.chk") + if not os.path.exists(backup_chk): + break + if i == 999: + raise RuntimeError("Too many used checkpoint files.") + backup_counter += 1 + # Backup checkpoint + print(f"Making backup for used checkpoint file past_checkpoints/checkpoint_used_{backup_counter:03d}.chk") + os.system(f"cp {checkpoint_path} {backup_chk}") + else: + # Ensure backup directory exists + backup_dir = os.path.join(toPath, "backup") + os.makedirs(backup_dir, exist_ok=True) + # Define files to backup: (source_path, backup_prefix, description) + files_to_backup = [ + (output_path, "output", "log file"), + (movie_dcd_path, "movie", "dcd file"), + (checkpoint_path, "checkpoint", "checkpoint file"), + (info_dat_path, "info", "info file"), + (time_dat_path, "time", "time file") + ] + + # Find the next available backup number + backup_counter = 0 + for i in range(1000): + backup_paths = [os.path.join(backup_dir, f"{prefix}_{backup_counter:03d}.{ext}") + for _, prefix, _ in files_to_backup + for ext in (['log'] if prefix == 'output' else + ['dcd'] if prefix == 'movie' else + ['chk'] if prefix == 'checkpoint' else ['dat'])] + if not any(os.path.exists(path) for path in backup_paths): + break + if i == 999: + raise RuntimeError("Too many backup files.") + backup_counter += 1 + + # Backup all files + for source_path, prefix, description in files_to_backup: + if os.path.exists(source_path): + ext = 'log' if prefix == 'output' else 'dcd' if prefix == 'movie' else 'chk' if prefix == 'checkpoint' else 'dat' + backup_path = os.path.join(backup_dir, f"{prefix}_{backup_counter:03d}.{ext}") + print(f"Making backup {description} backup/{prefix}_{backup_counter:03d}.{ext}") + os.system(f"cp {source_path} {backup_path}") + + + simulation.reporters.append(StateDataReporter(sys.stdout, args.reportInterval, step=True, potentialEnergy=True, temperature=True, append=reporter_append)) # output energy and temperature during simulation to terminal + simulation.reporters.append(StateDataReporter(output_path, args.reportInterval, step=True, potentialEnergy=True, temperature=True, append=reporter_append)) # output energy and temperature to a file + simulation.reporters.append(PDBReporter(movie_pdb_path, reportInterval=args.reportInterval)) # output PDBs of simulated structures; deprecated (see https://github.com/cabb99/openawsem/issues/86) + simulation.reporters.append(DCDReporter(movie_dcd_path, reportInterval=args.reportInterval, append=True)) # output PDBs of simulated structures. DCD is appending to the minimization output if it exists + simulation.reporters.append(CheckpointReporter(checkpoint_path, args.checkpointInterval)) # save progress during the simulation + + if args.dryRun: + if args.simulation_mode == 1: # test temperature setting + deltaT = (Tend - Tstart) / args.numFrames + for i in range(args.numFrames): + integrator.setTemperature((Tstart + deltaT*i)*kelvin) + raise SystemExit("Simulation configured successfully") + + print("Simulation Starts") + start_time = time.time() + + if args.simulation_mode == 0: + simulation.step(int(args.steps)) + elif args.simulation_mode == 1: + deltaT = (Tend - Tstart) / args.numFrames + for i in range(args.numFrames): + integrator.setTemperature((Tstart + deltaT*i)*kelvin) + simulation.step(args.reportInterval) + + # simulation.saveCheckpoint('step_%d.chk' % i) + # simulation.context.setParameter("k_membrane", 0) + # if i < snapShotCount/2: + # simulation.context.setParameter("k_membrane", (i % 2) * k_mem) + # simulation.context.setParameter("k_single_helix_orientation_bias", (i % 2) * k_single_helix_orientation_bias) + # else: + # simulation.context.setParameter("k_membrane", k_mem) + # simulation.context.setParameter("k_single_helix_orientation_bias", k_single_helix_orientation_bias) + + # simulation.context.setParameter("k_membrane", (i)*(k_mem/snapShotCount)) + # simulation.context.setParameter("k_single_helix_orientation_bias", (i)*(k_single_helix_orientation_bias/snapShotCount)) + # print(simulation.context.getParameter("k_membrane")) + + + # simulation.step(int(1e6)) + + time_taken = time.time() - start_time # time_taken is in seconds + hours, rest = divmod(time_taken,3600) + minutes, seconds = divmod(rest, 60) + print(f"---{hours} hours {minutes} minutes {seconds} seconds ---") + + with open(time_dat_path, "w") as out: + out.write(str(time_taken)+"\n") + + # accompany with analysis run + simulation = None + time.sleep(10) + os.chdir(pwd) + print(os.getcwd()) + if args.fasta == "": + analysis_fasta = "" + else: + analysis_fasta = f"--fasta {args.fasta}" + additional_cmd = "" + if args.includeLigands: + additional_cmd += "--includeLigands " + if args.periodic_box: + additional_cmd += f"--periodic_box {' '.join(map(str, args.periodic_box))} " + if args.fixed_residue_indices: + additional_cmd += f"--fixed_residue_indices {fixed_residue_indices} " + if args.fromOpenMMPDB: + additional_cmd += f"--fromOpenMMPDB " + os.system(f"{sys.executable} mm_analyze.py {args.protein} -t {os.path.join(toPath, 'movie.dcd')} --subMode {args.subMode} -f {args.forces} {analysis_fasta} {additional_cmd} -c {chain} --output {info_dat_path}") + + + + +def main(args=None): + parser = argparse.ArgumentParser( + description="This is a python3 script to automatically copy the template file and run simulations") + # default=False with action="store_true" is redundant but doesn't hurt us + parser.add_argument("protein", help="The name of the protein") + parser.add_argument("--name", default="simulation", help="Name of the simulation") + parser.add_argument("--to", default="./", help="location of movie file") + parser.add_argument("-c", "--chain", type=str, default="-1") + parser.add_argument("-t", "--thread", type=int, default=-1, help="default is using all that is available") + parser.add_argument("-p", "--platform", type=str, default="OpenCL", choices=["OpenCL", "CPU", "HIP", "Reference", "CUDA"], help="Platform to run the simulation.") + parser.add_argument("-s", "--steps", type=float, default=1e7, help="step size, default 1e7") + parser.add_argument("--tempStart", type=float, default=800, help="Starting temperature") + parser.add_argument("--tempEnd", type=float, default=200, help="Ending temperature") + parser.add_argument("--fromCheckPoint", type=str, default=None, help="The checkpoint file you want to start from") + parser.add_argument("-m", "--simulation_mode", type=int, default=1, + help="default 1,\ + 0: constant temperature,\ + 1: temperature annealing") + parser.add_argument("--subMode", type=int, default=-1) + parser.add_argument("-f", "--forces", default="forces_setup.py") + parser.add_argument("--parameters", default=None) + parser.add_argument("-r", "--reportInterval", "--reportFrequency", type=float, default=None, help="Number of steps between each frame recorded") + parser.add_argument("--checkpointInterval", type=float, default=None, help="Number of steps between each frame recorded") + parser.add_argument("--checkpointFile", type=str, default="checkpoint.chk", help="Name of the checkpoint file") + parser.add_argument("--numFrames", type=int, default=400, help="Number of frames to record. Can be overridden by --reportInterval") + parser.add_argument("--fromOpenMMPDB", action="store_true", default=False) + parser.add_argument("--fasta", type=str, default="crystal_structure.fasta") + parser.add_argument("--timeStep", type=int, default=2, help="time step in femtoseconds") + parser.add_argument("--includeLigands", action="store_true", default=False) + parser.add_argument('--device', default=0, help='OpenCL/CUDA device index') + parser.add_argument('--removeCMMotionRemover', action="store_true", default=False, help='Removes CMMotionRemover. Recommended for periodic boundary conditions and membrane simulations') + parser.add_argument('--fixed_residue_indices', type=str, default='', help='csv file with indices (not "ids" or "resnums") of residues whose positions should be fixed)') + parser.add_argument('--periodic_box', type=float, nargs=3, metavar=('X', 'Y', 'Z'), help='Enable periodic boundary conditions with box dimensions in x, y, z (nanometers)') + parser.add_argument('--dryRun',action="store_true",default=False,help="Return the configuration and exit without running the simulation") + + if args is None: + args = parser.parse_args() + else: + args = parser.parse_args(args) + + with open('commandline_args.txt', 'a') as f: + f.write(' '.join(sys.argv)) + f.write('\n') + print(' '.join(sys.argv)) + + # Correct number of timesteps if negative + if args.steps <= 0: + logging.warning("--steps must be a positive integer. Reverting to default 1e7") + args.steps = 1e7 + else: + # Convert steps to integer + args.steps = int(args.steps) + + # Adds a deprecation warning if the deprecated option '--reportFrequency' is used + if '--reportFrequency' in sys.argv: + logging.warning("The '--reportFrequency' option is deprecated. Please use '--reportInterval' instead.", DeprecationWarning) + + if args.reportInterval is None and args.numFrames>0: + #Report interval is not specified and number of frames is reasonable + if args.numFrames > args.steps: + logging.warning("Number of frames --numFrames is more than number of steps. Setting number of frames to {args.steps}.") + args.numFrames = args.steps + + args.reportInterval = math.ceil(args.steps / args.numFrames) + new_steps = int(args.reportInterval * args.numFrames) + if new_steps != args.steps: + logging.warning(f"Number of frames --reportInterval does not divide number of steps --steps exactly. Adjusting number of steps from {args.steps} to {new_steps}") + args.steps = new_steps + elif args.reportInterval is not None and args.reportInterval > 0: + #Report interval is specified and is reasonable + if '--numFrames' in sys.argv: + logging.warning("Ignoring user-specified --numFrames. --reportInterval takes priority over --numFrames. ") + args.numFrames = math.ceil(args.steps / args.reportInterval) + new_steps = int(args.numFrames * args.reportInterval) + if new_steps != args.steps: + logging.warning(f"Number of frames --numFrames does not divide number of steps --steps exactly. Adjusting number of steps from {args.steps} to {new_steps}") + args.steps = new_steps + elif args.numFrames == 0 and args.reportInterval is None: + logging.info("No frames will be recorded. Simulation will run for the specified number of steps.") + else: + logging.error("Invalid values: Either --reportInterval or --numFrames must be provided with positive values.") + raise ValueError("Both --reportInterval and --numFrames cannot be missing or zero. Please provide valid inputs.") + + args.reportInterval = int(args.reportInterval) + args.checkpointInterval = args.reportInterval if args.checkpointInterval is None else int(args.checkpointInterval) + + if args.dryRun: + print("Dry run mode. Simulation will not run.") + print(args) + return args + + run(args) + +if __name__=="__main__": + main() diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/2mlt_frag1/original_pdbs/2mlt_frag1.pdb b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/2mlt_frag1/original_pdbs/2mlt_frag1.pdb new file mode 100644 index 00000000..6913f62a --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/2mlt_frag1/original_pdbs/2mlt_frag1.pdb @@ -0,0 +1,104 @@ +CRYST1 60.832 38.293 42.211 90.00 90.00 90.00 C 2 2 21 16 +ORIGX1 1.000000 0.000000 0.000000 0.00000 +ORIGX2 0.000000 1.000000 0.000000 0.00000 +ORIGX3 0.000000 0.000000 1.000000 0.00000 +SCALE1 0.016439 0.000000 0.000000 0.00000 +SCALE2 0.000000 0.026114 0.000000 0.00000 +SCALE3 0.000000 0.000000 0.023691 0.00000 +MTRIX1 1 -0.996310 -0.033870 -0.078870 71.25100 1 +MTRIX2 1 0.048050 -0.981470 -0.185470 2.71100 1 +MTRIX3 1 -0.071130 -0.188580 0.979480 2.05300 1 +ATOM 1 N GLY A 1 42.375 -12.180 24.780 1.00 35.31 N +ATOM 2 CA GLY A 1 43.603 -11.488 24.325 1.00 35.57 C +ATOM 3 C GLY A 1 43.288 -10.171 23.615 1.00 34.64 C +ATOM 4 O GLY A 1 42.111 -9.896 23.277 1.00 35.82 O +ATOM 5 N ILE A 2 44.323 -9.391 23.299 1.00 32.23 N +ATOM 6 CA ILE A 2 44.200 -8.183 22.475 1.00 27.55 C +ATOM 7 C ILE A 2 43.750 -8.629 21.119 1.00 24.92 C +ATOM 8 O ILE A 2 43.068 -7.904 20.409 1.00 23.73 O +ATOM 9 CB ILE A 2 45.525 -7.320 22.425 1.00 30.10 C +ATOM 10 CG1 ILE A 2 45.924 -6.837 23.820 1.00 29.64 C +ATOM 11 CG2 ILE A 2 45.555 -6.173 21.386 1.00 30.54 C +ATOM 12 CD1 ILE A 2 44.837 -6.338 24.762 1.00 32.44 C +ATOM 13 N GLY A 3 44.161 -9.867 20.749 1.00 22.69 N +ATOM 14 CA GLY A 3 43.999 -10.264 19.329 1.00 21.05 C +ATOM 15 C GLY A 3 42.433 -10.405 19.166 1.00 22.08 C +ATOM 16 O GLY A 3 41.912 -10.061 18.096 1.00 22.86 O +ATOM 17 N ALA A 4 41.862 -10.961 20.191 1.00 21.60 N +ATOM 18 CA ALA A 4 40.378 -11.260 20.106 1.00 21.80 C +ATOM 19 C ALA A 4 39.584 -9.950 20.087 1.00 21.67 C +ATOM 20 O ALA A 4 38.676 -9.747 19.278 1.00 22.21 O +ATOM 21 CB ALA A 4 40.061 -12.080 21.350 1.00 22.97 C +ATOM 22 N VAL A 5 39.936 -9.001 20.956 1.00 22.13 N +ATOM 23 CA VAL A 5 39.355 -7.658 21.083 1.00 19.34 C +ATOM 24 C VAL A 5 39.536 -6.896 19.795 1.00 18.81 C +ATOM 25 O VAL A 5 38.626 -6.314 19.126 1.00 17.22 O +ATOM 26 CB VAL A 5 39.843 -6.933 22.338 1.00 20.40 C +ATOM 27 CG1 VAL A 5 39.237 -5.519 22.413 1.00 23.06 C +ATOM 28 CG2 VAL A 5 39.745 -7.587 23.653 1.00 21.67 C +ATOM 29 N LEU A 6 40.752 -7.021 19.222 1.00 16.05 N +ATOM 30 CA LEU A 6 41.062 -6.432 17.957 1.00 17.59 C +ATOM 31 C LEU A 6 40.230 -6.935 16.870 1.00 20.01 C +ATOM 32 O LEU A 6 39.649 -6.121 16.029 1.00 21.90 O +ATOM 33 CB LEU A 6 42.627 -6.461 17.880 1.00 24.58 C +ATOM 34 CG LEU A 6 43.125 -6.023 16.524 1.00 23.91 C +ATOM 35 CD1 LEU A 6 42.706 -4.584 16.210 1.00 27.44 C +ATOM 36 CD2 LEU A 6 44.669 -6.152 16.638 1.00 29.31 C +ATOM 37 N LYS A 7 39.981 -8.229 16.721 1.00 19.83 N +ATOM 38 CA LYS A 7 39.079 -8.646 15.636 1.00 22.55 C +ATOM 39 C LYS A 7 37.648 -8.063 15.784 1.00 19.04 C +ATOM 40 O LYS A 7 37.031 -7.839 14.731 1.00 21.18 O +ATOM 41 CB LYS A 7 38.854 -10.176 15.616 1.00 27.62 C +ATOM 42 CG LYS A 7 40.011 -10.993 15.144 1.00 40.15 C +ATOM 43 CD LYS A 7 39.691 -12.487 15.325 1.00 47.84 C +ATOM 44 CE LYS A 7 40.599 -13.394 14.493 1.00 53.11 C +ATOM 45 NZ LYS A 7 39.966 -14.755 14.319 1.00 55.47 N +ATOM 46 N VAL A 8 37.111 -7.988 16.981 1.00 19.69 N +ATOM 47 CA VAL A 8 35.792 -7.369 17.211 1.00 20.52 C +ATOM 48 C VAL A 8 35.776 -5.881 16.885 1.00 20.31 C +ATOM 49 O VAL A 8 34.775 -5.402 16.257 1.00 20.12 O +ATOM 50 CB VAL A 8 35.113 -7.600 18.562 1.00 23.09 C +ATOM 51 CG1 VAL A 8 34.774 -9.045 18.851 1.00 24.22 C +ATOM 52 CG2 VAL A 8 35.769 -6.970 19.726 1.00 27.95 C +ATOM 53 N LEU A 9 36.860 -5.176 17.216 1.00 19.55 N +ATOM 54 CA LEU A 9 36.899 -3.759 16.725 1.00 16.83 C +ATOM 55 C LEU A 9 36.778 -3.644 15.254 1.00 19.11 C +ATOM 56 O LEU A 9 36.328 -2.551 14.694 1.00 19.69 O +ATOM 57 CB LEU A 9 38.227 -3.088 17.147 1.00 16.57 C +ATOM 58 CG LEU A 9 38.462 -3.091 18.615 1.00 18.69 C +ATOM 59 CD1 LEU A 9 39.783 -2.288 18.873 1.00 24.09 C +ATOM 60 CD2 LEU A 9 37.265 -2.535 19.351 1.00 22.17 C +ATOM 61 N THR A 10 37.320 -4.627 14.530 1.00 19.39 N +ATOM 62 CA THR A 10 37.338 -4.508 13.084 1.00 19.41 C +ATOM 63 C THR A 10 36.072 -5.022 12.458 1.00 21.08 C +ATOM 64 O THR A 10 35.694 -4.554 11.333 1.00 21.48 O +ATOM 65 CB THR A 10 38.687 -5.179 12.486 1.00 24.07 C +ATOM 66 OG1 THR A 10 38.285 -6.538 12.354 1.00 31.20 O +ATOM 67 CG2 THR A 10 39.877 -5.049 13.451 1.00 20.75 C +ATOM 68 N THR A 11 35.315 -5.870 13.113 1.00 21.12 N +ATOM 69 CA THR A 11 34.132 -6.405 12.343 1.00 24.14 C +ATOM 70 C THR A 11 32.874 -6.299 13.140 1.00 24.13 C +ATOM 71 O THR A 11 31.823 -5.889 12.630 1.00 27.78 O +ATOM 72 CB THR A 11 34.462 -7.925 11.935 1.00 27.78 C +ATOM 73 OG1 THR A 11 34.702 -8.591 13.199 1.00 31.22 O +ATOM 74 CG2 THR A 11 35.695 -7.959 11.047 1.00 30.31 C +ATOM 75 N GLY A 12 32.918 -6.606 14.420 1.00 23.00 N +ATOM 76 CA GLY A 12 31.584 -6.595 15.140 1.00 24.17 C +ATOM 77 C GLY A 12 31.264 -5.168 15.584 1.00 24.45 C +ATOM 78 O GLY A 12 30.060 -4.914 15.603 1.00 23.79 O +ATOM 79 N LEU A 13 32.195 -4.276 15.948 1.00 22.05 N +ATOM 80 CA LEU A 13 31.923 -2.919 16.364 1.00 23.24 C +ATOM 81 C LEU A 13 31.251 -2.004 15.324 1.00 21.24 C +ATOM 82 O LEU A 13 30.232 -1.308 15.679 1.00 23.02 O +ATOM 83 CB LEU A 13 33.146 -2.183 17.008 1.00 25.55 C +ATOM 84 CG LEU A 13 32.913 -1.523 18.351 1.00 27.01 C +ATOM 85 CD1 LEU A 13 33.999 -0.517 18.760 1.00 27.53 C +ATOM 86 CD2 LEU A 13 31.587 -0.842 18.531 1.00 24.54 C +ATOM 87 N PRO A 14 31.689 -1.979 14.106 1.00 17.38 N +ATOM 88 CA PRO A 14 31.026 -1.278 13.030 1.00 17.52 C +ATOM 89 C PRO A 14 29.521 -1.670 12.857 1.00 18.98 C +ATOM 90 O PRO A 14 28.657 -0.801 12.744 1.00 16.75 O +ATOM 91 CB PRO A 14 31.845 -1.614 11.816 1.00 17.80 C +ATOM 92 CG PRO A 14 33.118 -2.205 12.303 1.00 18.05 C +ATOM 93 CD PRO A 14 33.098 -2.363 13.769 1.00 17.96 C +END diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/2mlt_frag1/para_HB b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/2mlt_frag1/para_HB new file mode 100644 index 00000000..df4195dc --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/2mlt_frag1/para_HB @@ -0,0 +1,41 @@ + 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 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a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/gamma.dat b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/gamma.dat new file mode 100644 index 00000000..ebe8e61b --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/gamma.dat @@ -0,0 +1,421 @@ + 0.72008 0.72008 +-0.27029 -0.27029 +-0.25968 -0.25968 +-0.40222 -0.40222 + 0.62053 0.62053 +-0.24469 -0.24469 +-0.34851 -0.34851 +-0.11391 -0.11391 +-0.12511 -0.12511 + 1.00000 1.00000 + 1.00000 1.00000 +-0.45156 -0.45156 + 0.50732 0.50732 + 0.56857 0.56857 +-0.53459 -0.53459 +-0.20625 -0.20625 + 0.08004 0.08004 + 0.39663 0.39663 + 0.11183 0.11183 + 0.91795 0.91795 +-0.64172 -0.64172 +-0.28113 -0.28113 + 0.40922 0.40922 +-0.40038 -0.40038 +-0.20918 -0.20918 +-0.03378 -0.03378 +-0.32864 -0.32864 +-0.53414 -0.53414 +-0.13629 -0.13629 +-0.25104 -0.25104 +-0.95588 -0.95588 +-0.01696 -0.01696 +-0.17514 -0.17514 +-0.82493 -0.82493 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+-0.05899 -0.36672 +-0.10044 0.19480 + 0.42645 -1.00000 + 0.15157 -0.94841 + 0.43719 1.00000 + 0.21090 -0.44608 + 0.59308 0.37531 + 0.73327 0.86844 diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/lammps_movie.dcd b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/lammps_movie.dcd new file mode 100644 index 00000000..c54b2aa6 Binary files /dev/null and b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/lammps_movie.dcd differ diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/lammps_movie.pdb b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/lammps_movie.pdb new file mode 100644 index 00000000..bb5ba66d --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/lammps_movie.pdb @@ -0,0 +1,79 @@ +MODEL 1 +ATOM 1 CA GLY A 1 43.603 -11.488 24.325 1.00 0.00 C +ATOM 2 C GLY A 1 43.264 -10.199 23.553 1.00 0.00 C +ATOM 3 O GLY A 1 42.111 -9.896 23.277 1.00 0.00 O +ATOM 4 N ILE A 2 44.303 -9.461 23.22 1.00 0.00 N +ATOM 5 H ILE A 2 45.234 -9.706 23.444 1.00 0.00 H +ATOM 6 CA ILE A 2 44.2 -8.183 22.475 1.00 0.00 C +ATOM 7 C ILE A 2 43.789 -8.583 21.072 1.00 0.00 C +ATOM 8 O ILE A 2 43.068 -7.904 20.409 1.00 0.00 O +ATOM 9 CB ILE A 2 45.525 -7.32 22.425 1.00 0.00 C +ATOM 10 N GLY A 3 44.271 -9.699 20.648 1.00 0.00 N +ATOM 11 H GLY A 3 44.854 -10.247 21.184 1.00 0.00 H +ATOM 12 CA GLY A 3 43.999 -10.264 19.329 1.00 0.00 C +ATOM 13 C GLY A 3 42.477 -10.433 19.116 1.00 0.00 C +ATOM 14 O GLY A 3 41.912 -10.061 18.096 1.00 0.00 O +ATOM 15 N ALA A 4 41.843 -11.003 20.106 1.00 0.00 N +ATOM 16 H ALA A 4 42.3 -11.303 20.929 1.00 0.00 H +ATOM 17 CA ALA A 4 40.378 -11.26 20.106 1.00 0.00 C +ATOM 18 C ALA A 4 39.591 -9.927 20.07 1.00 0.00 C +ATOM 19 O ALA A 4 38.676 -9.747 19.278 1.00 0.00 O +ATOM 20 CB ALA A 4 40.061 -12.08 21.35 1.00 0.00 C +ATOM 21 N VAL A 5 39.977 -9.009 20.948 1.00 0.00 N +ATOM 22 H VAL A 5 40.716 -9.155 21.587 1.00 0.00 H +ATOM 23 CA VAL A 5 39.355 -7.658 21.083 1.00 0.00 C +ATOM 24 C VAL A 5 39.522 -6.938 19.719 1.00 0.00 C +ATOM 25 O VAL A 5 38.626 -6.314 19.126 1.00 0.00 O +ATOM 26 CB VAL A 5 39.843 -6.933 22.338 1.00 0.00 C +ATOM 27 N LEU A 6 40.693 -7.047 19.25 1.00 0.00 N +ATOM 28 H LEU A 6 41.417 -7.55 19.729 1.00 0.00 H +ATOM 29 CA LEU A 6 41.062 -6.432 17.957 1.00 0.00 C +ATOM 30 C LEU A 6 40.142 -6.853 16.792 1.00 0.00 C +ATOM 31 O LEU A 6 39.649 -6.121 16.029 1.00 0.00 O +ATOM 32 CB LEU A 6 42.627 -6.461 17.88 1.00 0.00 C +ATOM 33 N LYS A 7 39.932 -8.047 16.685 1.00 0.00 N +ATOM 34 H LYS A 7 40.331 -8.638 17.301 1.00 0.00 H +ATOM 35 CA LYS A 7 39.079 -8.646 15.636 1.00 0.00 C +ATOM 36 C LYS A 7 37.648 -8.086 15.716 1.00 0.00 C +ATOM 37 O LYS A 7 37.031 -7.839 14.731 1.00 0.00 O +ATOM 38 CB LYS A 7 38.854 -10.176 15.616 1.00 0.00 C +ATOM 39 N VAL A 8 37.151 -7.899 16.913 1.00 0.00 N +ATOM 40 H VAL A 8 37.65 -8.099 17.708 1.00 0.00 H +ATOM 41 CA VAL A 8 35.792 -7.369 17.211 1.00 0.00 C +ATOM 42 C VAL A 8 35.726 -5.888 16.79 1.00 0.00 C +ATOM 43 O VAL A 8 34.775 -5.402 16.257 1.00 0.00 O +ATOM 44 CB VAL A 8 35.113 -7.6 18.562 1.00 0.00 C +ATOM 45 N LEU A 9 36.761 -5.197 17.048 1.00 0.00 N +ATOM 46 H LEU A 9 37.529 -5.589 17.478 1.00 0.00 H +ATOM 47 CA LEU A 9 36.899 -3.759 16.725 1.00 0.00 C +ATOM 48 C LEU A 9 36.819 -3.547 15.216 1.00 0.00 C +ATOM 49 O LEU A 9 36.328 -2.551 14.694 1.00 0.00 O +ATOM 50 CB LEU A 9 38.227 -3.088 17.147 1.00 0.00 C +ATOM 51 N THR A 10 37.316 -4.511 14.544 1.00 0.00 N +ATOM 52 H THR A 10 37.713 -5.315 14.965 1.00 0.00 H +ATOM 53 CA THR A 10 37.338 -4.508 13.084 1.00 0.00 C +ATOM 54 C THR A 10 36.056 -4.969 12.347 1.00 0.00 C +ATOM 55 O THR A 10 35.694 -4.554 11.333 1.00 0.00 O +ATOM 56 CB THR A 10 38.687 -5.179 12.486 1.00 0.00 C +ATOM 57 N THR A 11 35.391 -5.834 12.89 1.00 0.00 N +ATOM 58 H THR A 11 35.684 -6.169 13.708 1.00 0.00 H +ATOM 59 CA THR A 11 34.132 -6.405 12.343 1.00 0.00 C +ATOM 60 C THR A 11 32.791 -6.284 13.093 1.00 0.00 C +ATOM 61 O THR A 11 31.823 -5.889 12.63 1.00 0.00 O +ATOM 62 CB THR A 11 34.462 -7.925 11.935 1.00 0.00 C +ATOM 63 N GLY A 12 32.772 -6.635 14.257 1.00 0.00 N +ATOM 64 H GLY A 12 33.554 -6.954 14.631 1.00 0.00 H +ATOM 65 CA GLY A 12 31.584 -6.595 15.14 1.00 0.00 C +ATOM 66 C GLY A 12 31.174 -5.191 15.577 1.00 0.00 C +ATOM 67 O GLY A 12 30.06 -4.914 15.603 1.00 0.00 O +ATOM 68 N LEU A 13 32.108 -4.323 15.915 1.00 0.00 N +ATOM 69 H LEU A 13 33.007 -4.547 15.894 1.00 0.00 H +ATOM 70 CA LEU A 13 31.923 -2.919 16.364 1.00 0.00 C +ATOM 71 C LEU A 13 31.169 -2.016 15.36 1.00 0.00 C +ATOM 72 O LEU A 13 30.232 -1.308 15.679 1.00 0.00 O +ATOM 73 CB LEU A 13 33.146 -2.183 17.008 1.00 0.00 C +ATOM 74 N PRO A 14 30.438 -0.95 13.712 1.00 0.00 N +ATOM 75 CA PRO A 14 31.026 -1.278 13.03 1.00 0.00 C +ATOM 76 O PRO A 14 28.657 -0.801 12.744 1.00 0.00 O +ATOM 77 CB PRO A 14 31.845 -1.614 11.816 1.00 0.00 C +ENDMDL diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/lammps_movie.psf b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/lammps_movie.psf new file mode 100644 index 00000000..2a79b919 --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/lammps_movie.psf @@ -0,0 +1,101 @@ +PSF + + 0 !NTITLE + + 77 !NATOM + 1 PROT 1 GLY CA C 0 1 0 + 2 PROT 1 GLY C C 0 1 0 + 3 PROT 1 GLY O O 0 1 0 + 4 PROT 2 ILE N N 0 1 0 + 5 PROT 2 ILE H H 0 1 0 + 6 PROT 2 ILE CA C 0 1 0 + 7 PROT 2 ILE C C 0 1 0 + 8 PROT 2 ILE O O 0 1 0 + 9 PROT 2 ILE CB C 0 1 0 + 10 PROT 3 GLY N N 0 1 0 + 11 PROT 3 GLY H H 0 1 0 + 12 PROT 3 GLY CA C 0 1 0 + 13 PROT 3 GLY C C 0 1 0 + 14 PROT 3 GLY O O 0 1 0 + 15 PROT 4 ALA N N 0 1 0 + 16 PROT 4 ALA H H 0 1 0 + 17 PROT 4 ALA CA C 0 1 0 + 18 PROT 4 ALA C C 0 1 0 + 19 PROT 4 ALA O O 0 1 0 + 20 PROT 4 ALA CB C 0 1 0 + 21 PROT 5 VAL N N 0 1 0 + 22 PROT 5 VAL H H 0 1 0 + 23 PROT 5 VAL CA C 0 1 0 + 24 PROT 5 VAL C C 0 1 0 + 25 PROT 5 VAL O O 0 1 0 + 26 PROT 5 VAL CB C 0 1 0 + 27 PROT 6 LEU N N 0 1 0 + 28 PROT 6 LEU H H 0 1 0 + 29 PROT 6 LEU CA C 0 1 0 + 30 PROT 6 LEU C C 0 1 0 + 31 PROT 6 LEU O O 0 1 0 + 32 PROT 6 LEU CB C 0 1 0 + 33 PROT 7 LYS N N 0 1 0 + 34 PROT 7 LYS H H 0 1 0 + 35 PROT 7 LYS CA C 0 1 0 + 36 PROT 7 LYS C C 0 1 0 + 37 PROT 7 LYS O O 0 1 0 + 38 PROT 7 LYS CB C 0 1 0 + 39 PROT 8 VAL N N 0 1 0 + 40 PROT 8 VAL H H 0 1 0 + 41 PROT 8 VAL CA C 0 1 0 + 42 PROT 8 VAL C C 0 1 0 + 43 PROT 8 VAL O O 0 1 0 + 44 PROT 8 VAL CB C 0 1 0 + 45 PROT 9 LEU N N 0 1 0 + 46 PROT 9 LEU H H 0 1 0 + 47 PROT 9 LEU CA C 0 1 0 + 48 PROT 9 LEU C C 0 1 0 + 49 PROT 9 LEU O O 0 1 0 + 50 PROT 9 LEU CB C 0 1 0 + 51 PROT 10 THR N N 0 1 0 + 52 PROT 10 THR H H 0 1 0 + 53 PROT 10 THR CA C 0 1 0 + 54 PROT 10 THR C C 0 1 0 + 55 PROT 10 THR O O 0 1 0 + 56 PROT 10 THR CB C 0 1 0 + 57 PROT 11 THR N N 0 1 0 + 58 PROT 11 THR H H 0 1 0 + 59 PROT 11 THR CA C 0 1 0 + 60 PROT 11 THR C C 0 1 0 + 61 PROT 11 THR O O 0 1 0 + 62 PROT 11 THR CB C 0 1 0 + 63 PROT 12 GLY N N 0 1 0 + 64 PROT 12 GLY H H 0 1 0 + 65 PROT 12 GLY CA C 0 1 0 + 66 PROT 12 GLY C C 0 1 0 + 67 PROT 12 GLY O O 0 1 0 + 68 PROT 13 LEU N N 0 1 0 + 69 PROT 13 LEU H H 0 1 0 + 70 PROT 13 LEU CA C 0 1 0 + 71 PROT 13 LEU C C 0 1 0 + 72 PROT 13 LEU O O 0 1 0 + 73 PROT 13 LEU CB C 0 1 0 + 74 PROT 14 PRO N N 0 1 0 + 75 PROT 14 PRO CA C 0 1 0 + 76 PROT 14 PRO O O 0 1 0 + 77 PROT 14 PRO CB C 0 1 0 + + 66 !NBOND + 1 2 2 3 1 4 2 5 + 5 7 7 8 8 9 7 10 + 8 11 11 13 13 14 14 15 + 13 16 14 17 17 19 19 20 + 20 21 19 22 20 23 23 25 + 25 26 26 27 25 28 26 29 + 29 31 31 32 32 33 31 34 + 32 35 35 37 37 38 38 39 + 37 40 38 41 41 43 43 44 + 44 45 43 46 44 47 47 49 + 49 50 50 51 49 52 50 53 + 53 55 55 56 56 57 55 58 + 56 59 59 61 61 62 62 63 + 61 64 62 65 65 67 67 68 + 68 69 67 70 68 71 71 73 + 73 74 74 75 73 76 74 77 + 77 78 78 80 \ No newline at end of file diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/lammps_stdout.txt b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/lammps_stdout.txt new file mode 100644 index 00000000..a9f690b0 --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/lammps_stdout.txt @@ -0,0 +1,340 @@ +LAMMPS (29 Aug 2024 - Update 1) +Reading data file ... + orthogonal box = (-200 -200 -200) to (200 200 200) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 42 atoms + scanning bonds ... + 3 = max bonds/atom + orthogonal box = (-200.04 -200.04 -200.04) to (200.04 200.04 200.04) + 1 by 1 by 1 MPI processor grid + reading bonds ... + 54 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 1 1 + 5 = max # of 1-2 neighbors + 5 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.012 seconds +14 atoms in group alpha_carbons +14 atoms in group beta_atoms +14 atoms in group oxygens +Chain flag on +Chi flag on +Rama flag on +Rama_P flag on +SSWeight flag on +ABC flag on +Dssp_Hdrgn flag on +P_AP flag on +Water flag on +Burial flag on +Helix flag on + +Fix backbone Pair List cutoff 15.0000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: +- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419 +The log file lists these citations in BibTeX format. + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Generated 0 of 10 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 5 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14.5 + ghost atom cutoff = 25 + binsize = 7.25, bins = 3 2 2 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair vexcluded, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) fix backbone, perpetual + attributes: half, newton on, cut 25 + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Setting up Verlet run ... + Unit style : real + Current step : 0 + Time step : 2 +theta: 0.999902 +theta: 0.907789 +theta: 0.977168 +theta: 2.95718e-11 +theta: 9.51791e-06 +theta: 0.999987 +theta: 0.999998 +theta: 0.995307 +theta: 0.053473 +theta: 0.8969 +theta: 0.000277011 +theta: 0.99136 +theta: 3.46055e-05 +theta: 5.56847e-07 +theta: 0.99684 +theta: 0.0974702 +theta: 1.34021e-07 +theta: 0.999997 +theta: 0.014443 +theta: 1.84717e-05 +theta: 0.999779 +theta: 0.991874 +theta: 1.45192e-10 +theta: 1.59765e-06 +theta: 0.0882217 +theta: 0.999285 +theta: 0.99941 +theta: 3.98709e-10 +theta: 1.76004e-08 +theta: 0.999907 +theta: 1.4882e-12 +theta: 4.17318e-08 +theta: 2.36855e-08 +theta: 2.72717e-08 +theta: 1.79011e-08 +theta: 0.00934301 +theta: 0.999163 +ires: 0 + helix_par.kappa_sigma: 7 + helix_par.treshold: 3 + helix_ro[ires]: 2.88486 +ires: 1 + helix_par.kappa_sigma: 7 + helix_par.treshold: 3 + helix_ro[ires]: 1.99999 +ires: 2 + helix_par.kappa_sigma: 7 + helix_par.treshold: 3 + helix_ro[ires]: 2.94558 +ires: 3 + helix_par.kappa_sigma: 7 + helix_par.treshold: 3 + helix_ro[ires]: 1.89947 +ires: 4 + helix_par.kappa_sigma: 7 + helix_par.treshold: 3 + helix_ro[ires]: 4.06677 +ires: 5 + helix_par.kappa_sigma: 7 + helix_par.treshold: 3 + helix_ro[ires]: 2.06819 +ires: 6 + helix_par.kappa_sigma: 7 + helix_par.treshold: 3 + helix_ro[ires]: 3.87993 +ires: 7 + helix_par.kappa_sigma: 7 + helix_par.treshold: 3 + helix_ro[ires]: 3.08379 +ires: 8 + helix_par.kappa_sigma: 7 + helix_par.treshold: 3 + helix_ro[ires]: 2.09739 +ires: 9 + helix_par.kappa_sigma: 7 + helix_par.treshold: 3 + helix_ro[ires]: 1.01422 +ires: 10 + helix_par.kappa_sigma: 7 + helix_par.treshold: 3 + helix_ro[ires]: 1.08944 +ires: 11 + helix_par.kappa_sigma: 7 + helix_par.treshold: 3 + helix_ro[ires]: 1.99845 +ires: 12 + helix_par.kappa_sigma: 7 + helix_par.treshold: 3 + helix_ro[ires]: 1.99932 +ires: 13 + helix_par.kappa_sigma: 7 + helix_par.treshold: 3 + helix_ro[ires]: 1.00851 +se[j_resno]: V +xn[j]: 39.9773 -9.00925 20.9482 +xh[j]: 40.7164 -9.15472 21.5875 +dr_NO: 0.294391 +dr_HO: 0.156952 +dr_NO_sigma: 0.636658 +dr_HO_sigma: 0.271731 +R_NO: 3.28059 +helix_NO_zero: 2.9862 +R_HO: 2.31275 +helix_HO_zero: 2.1558 +helix_sigma_h[i_resno]: 0.833686 +helix_sigma_h[j_resno]: 3.26503e-07 +helix_gamma_p: 2 +helix_gamma_w: -1 +se[j_resno]: L +xn[j]: 40.6928 -7.04661 19.2501 +xh[j]: 41.417 -7.55012 19.7293 +dr_NO: -0.20781 +dr_HO: -0.335669 +dr_NO_sigma: -0.449416 +dr_HO_sigma: -0.581144 +R_NO: 2.77839 +helix_NO_zero: 2.9862 +R_HO: 1.82013 +helix_HO_zero: 2.1558 +helix_sigma_h[i_resno]: 0.999999 +helix_sigma_h[j_resno]: 0.999998 +helix_gamma_p: 2 +helix_gamma_w: -1 +se[j_resno]: K +xn[j]: 39.9323 -8.04728 16.6848 +xh[j]: 40.3311 -8.6377 17.3006 +dr_NO: 0.170671 +dr_HO: 0.115223 +dr_NO_sigma: 0.369099 +dr_HO_sigma: 0.199487 +R_NO: 3.15687 +helix_NO_zero: 2.9862 +R_HO: 2.27102 +helix_HO_zero: 2.1558 +helix_sigma_h[i_resno]: 0.681755 +helix_sigma_h[j_resno]: 4.46578e-06 +helix_gamma_p: 2 +helix_gamma_w: -1 +se[j_resno]: V +xn[j]: 37.1505 -7.89867 16.913 +xh[j]: 37.6496 -8.09854 17.7077 +dr_NO: 0.380817 +dr_HO: 0.341568 +dr_NO_sigma: 0.823567 +dr_HO_sigma: 0.591358 +R_NO: 3.36702 +helix_NO_zero: 2.9862 +R_HO: 2.49737 +helix_HO_zero: 2.1558 +helix_sigma_h[i_resno]: 1 +helix_sigma_h[j_resno]: 0.236293 +helix_gamma_p: 2 +helix_gamma_w: -1 +se[j_resno]: L +xn[j]: 36.7614 -5.19712 17.0477 +xh[j]: 37.5294 -5.58949 17.4784 +dr_NO: 0.0210315 +dr_HO: -0.0481428 +dr_NO_sigma: 0.0454833 +dr_HO_sigma: -0.0833498 +R_NO: 3.00723 +helix_NO_zero: 2.9862 +R_HO: 2.10766 +helix_HO_zero: 2.1558 +helix_sigma_h[i_resno]: 3.26503e-07 +helix_sigma_h[j_resno]: 0.999997 +helix_gamma_p: 2 +helix_gamma_w: -1 +se[j_resno]: T +xn[j]: 37.3155 -4.5111 14.5436 +xh[j]: 37.7126 -5.31463 14.9654 +dr_NO: 0.214313 +dr_HO: 0.195981 +dr_NO_sigma: 0.463479 +dr_HO_sigma: 0.339302 +R_NO: 3.20051 +helix_NO_zero: 2.9862 +R_HO: 2.35178 +helix_HO_zero: 2.1558 +helix_sigma_h[i_resno]: 0.999998 +helix_sigma_h[j_resno]: 1 +helix_gamma_p: 2 +helix_gamma_w: -1 +se[j_resno]: T +xn[j]: 35.3911 -5.83371 12.8898 +xh[j]: 35.6843 -6.1685 13.7083 +dr_NO: 0.191923 +dr_HO: 0.2212 +dr_NO_sigma: 0.415059 +dr_HO_sigma: 0.382964 +R_NO: 3.17812 +helix_NO_zero: 2.9862 +R_HO: 2.377 +helix_HO_zero: 2.1558 +helix_sigma_h[i_resno]: 4.46578e-06 +helix_sigma_h[j_resno]: 1 +helix_gamma_p: 2 +helix_gamma_w: -1 +se[j_resno]: G +xn[j]: 32.7717 -6.63505 14.257 +xh[j]: 33.5537 -6.9538 14.6308 +dr_NO: 0.101418 +dr_HO: 0.40234 +dr_NO_sigma: 0.219329 +dr_HO_sigma: 0.696572 +R_NO: 3.08762 +helix_NO_zero: 2.9862 +R_HO: 2.55814 +helix_HO_zero: 2.1558 +helix_sigma_h[i_resno]: 0.236293 +helix_sigma_h[j_resno]: 0.999999 +helix_gamma_p: 2 +helix_gamma_w: -1 +se[j_resno]: L +xn[j]: 32.1077 -4.32336 15.9151 +xh[j]: 33.0074 -4.54661 15.8943 +dr_NO: 1.75124 +dr_HO: 1.90001 +dr_NO_sigma: 3.78729 +dr_HO_sigma: 3.2895 +R_NO: 4.73744 +helix_NO_zero: 2.9862 +R_HO: 4.05581 +helix_HO_zero: 2.1558 +helix_sigma_h[i_resno]: 0.999997 +helix_sigma_h[j_resno]: 0.999999 +helix_gamma_p: 2 +helix_gamma_w: -1 +se[j_resno]: P +xn[j]: 31.6086 -2.06535 14.1476 +xh[j]: 32.3653 -2.63615 13.8907 +dr_NO: 2.5641 +dr_HO: 2.45946 +dr_NO_sigma: 5.54521 +dr_HO_sigma: 4.25807 +R_NO: 5.5503 +helix_NO_zero: 2.9862 +R_HO: 4.61526 +helix_HO_zero: 2.1558 +helix_sigma_h[i_resno]: 1 +helix_sigma_h[j_resno]: 1 +helix_gamma_p: 2 +helix_gamma_w: -1 +Per MPI rank memory allocation (min/avg/max) = 7.178 | 7.178 | 7.178 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 0 300 2.1331833 184.92302 223.72017 -35334.618 2775.6115 +Loop time of 7.48e-07 on 1 procs for 0 steps with 42 atoms + +0.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Bond | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 7.48e-07 | | |100.00 + +Nlocal: 42 ave 42 max 42 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 699 ave 699 max 699 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 699 +Ave neighs/atom = 16.642857 +Ave special neighs/atom = 2.5714286 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/log.lammps b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/log.lammps new file mode 100644 index 00000000..011a476b --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/log.lammps @@ -0,0 +1,155 @@ +LAMMPS (29 Aug 2024 - Update 1) +# 3d protein simulation + +units real + +timestep 2 + +dimension 3 + +boundary s s s +#boundary p p p + +neighbor 10 bin +neigh_modify delay 5 + +atom_modify sort 0 0.0 + +special_bonds fene + +atom_style awsemmd + +bond_style harmonic + +pair_style vexcluded 2 3.5 3.5 + +read_data data.2mlt_frag1 +Reading data file ... + orthogonal box = (-200 -200 -200) to (200 200 200) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 42 atoms + scanning bonds ... + 3 = max bonds/atom + orthogonal box = (-200.04 -200.04 -200.04) to (200.04 200.04 200.04) + 1 by 1 by 1 MPI processor grid + reading bonds ... + 54 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 1 1 + 5 = max # of 1-2 neighbors + 5 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.012 seconds + +pair_coeff * * 0.0 +pair_coeff 1 1 20.0 3.5 4.5 +pair_coeff 1 4 20.0 3.5 4.5 +pair_coeff 4 4 20.0 3.5 4.5 +pair_coeff 3 3 20.0 3.5 3.5 + + +velocity all create 300.0 2349852 + +group alpha_carbons id 1 4 7 10 13 16 19 22 25 28 31 34 37 40 +14 atoms in group alpha_carbons + +group beta_atoms id 3 6 9 12 15 18 21 24 27 30 33 36 39 42 +14 atoms in group beta_atoms + +group oxygens id 2 5 8 11 14 17 20 23 26 29 32 35 38 41 +14 atoms in group oxygens + + +fix 1 all nvt temp 300.0 300.0 100.0 +fix 2 alpha_carbons backbone beta_atoms oxygens fix_backbone_coeff.data 2mlt_frag1.seq +Chain flag on +Chi flag on +Rama flag on +Rama_P flag on +SSWeight flag on +ABC flag on +Dssp_Hdrgn flag on +P_AP flag on +Water flag on +Burial flag on +Helix flag on + +Fix backbone Pair List cutoff 15.0000 + +thermo 1000 +dump 1 all atom 1000 dump.lammpstrj + +dump_modify 1 sort id + +reset_timestep 0 +run 0 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419 + +@Article{Gissinger24, + author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor}, + title = {Type Label Framework for Bonded Force Fields in LAMMPS}, + journal = {J. Phys. Chem. B}, + year = 2024, + volume = 128, + number = 13, + pages = {3282–-3297} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Generated 0 of 10 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 5 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14.5 + ghost atom cutoff = 25 + binsize = 7.25, bins = 3 2 2 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair vexcluded, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) fix backbone, perpetual + attributes: half, newton on, cut 25 + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 7.178 | 7.178 | 7.178 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 0 300 2.1331833 184.92302 223.72017 -35334.618 2775.6115 +Loop time of 7.48e-07 on 1 procs for 0 steps with 42 atoms + +0.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Bond | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 7.48e-07 | | |100.00 + +Nlocal: 42 ave 42 max 42 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 699 ave 699 max 699 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 699 +Ave neighs/atom = 16.642857 +Ave special neighs/atom = 2.5714286 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/para_HB b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/para_HB new file mode 100644 index 00000000..df4195dc --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/para_HB @@ -0,0 +1,41 @@ + 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 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-0.63993 + 0.00000 1.20939 0.00000 0.00000 1.03964 0.00000 0.00000 0.00000 1.53789 0.00000 -1.78384 0.00000 0.00000 0.00000 1.42011 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 1.60720 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 1.17581 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.80971 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 -1.85438 -1.17893 0.00000 0.00000 0.00000 -0.74379 0.00000 0.00000 0.00000 -1.70023 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 -0.59377 0.18153 diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/para_one b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/para_one new file mode 100644 index 00000000..9547ca68 --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/para_one @@ -0,0 +1,20 @@ + 4.59413901E-2 + -1.14228296 + -0.980181694 + -0.954810441 + 6.045979261E-2 + -0.940543473 + -0.944277942 + -0.326405674 + -0.517350674 + 0.674874783 + 0.559263945 + -1.37892628 + 0.311426193 + 0.229282543 + -0.544425964 + -0.59238559 + -0.701828241 + -0.337591201 + -0.414966911 + 0.660636663 diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/ssweight b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/ssweight new file mode 100644 index 00000000..a73aeb65 --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag1/ssweight @@ -0,0 +1,14 @@ +0.0 0.0 +0.0 0.0 +1.0 0.0 +1.0 0.0 +1.0 0.0 +1.0 0.0 +1.0 0.0 +1.0 0.0 +1.0 0.0 +1.0 0.0 +1.0 0.0 +0.0 0.0 +0.0 0.0 +0.0 0.0 diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2.coord b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2.coord new file mode 100644 index 00000000..694d81e3 --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2.coord @@ -0,0 +1,45 @@ +1 1 N 31.68899918 -1.97899997 14.10599995 N +2 1 C 31.02599907 -1.278 13.02999973 C-Alpha +3 1 C 29.52099991 -1.66999996 12.85700035 C-Prime +4 1 O 28.65699959 -0.801 12.74400043 O +5 1 C 31.84499931 -1.61399996 11.81599998 C-Beta +6 1 N 29.20700073 -2.9519999 12.86800003 N +7 1 C 27.8220005 -3.41799998 12.72399998 C-Alpha +8 1 C 27.02300072 -3.01600003 13.95100021 C-Prime +9 1 O 25.87199974 -2.55100012 13.76900005 O +10 1 C 27.74099922 -4.90600014 12.50199986 C-Beta +11 1 N 27.56999969 -3.1170001 15.12699986 N +12 1 C 26.95800018 -2.64899993 16.35099983 C-Alpha +13 1 C 26.61400032 -1.16900003 16.34399986 C-Prime +14 1 O 25.59900093 -0.73400003 16.93300056 O +15 1 C 27.81100082 -3.02699995 17.54199982 C-Beta +16 1 N 27.51399994 -0.36500001 15.79100037 N +17 1 C 27.34300041 1.05599999 15.61800003 C-Alpha +18 1 C 26.08099937 1.39199996 14.75800037 C-Prime +19 1 O 25.37999916 2.24000001 15.28199959 O +20 1 C 28.57900047 1.847 15.13199997 C-Beta +21 1 N 25.93000031 0.759 13.65699959 N +22 1 C 24.82500076 0.82700002 12.74400043 C-Alpha +23 1 C 23.49900055 0.405 13.43799973 C-Prime +24 1 O 22.55699921 1.16499996 13.35200024 O +25 1 C 25.07600021 0.039 11.49100018 C-Beta +26 1 N 23.51199913 -0.66100001 14.16100025 N +27 1 C 22.49200058 -1.08500004 15.08100033 C-Alpha +28 1 C 22.08300018 0.004 16.01199913 C-Prime +29 1 O 20.81999969 0.244 16.15999985 O +30 1 C 22.85400009 -2.41000009 15.7670002 C-Beta +31 1 N 22.93000031 0.59399998 16.82299995 N +32 1 C 22.62800026 1.63300002 17.76600075 C-Alpha +33 1 C 21.91699982 2.81900001 17.07999992 C-Prime +34 1 O 20.94199944 3.36500001 17.65500069 O +35 1 C 23.90200043 2.19199991 18.49900055 C-Beta +36 1 N 22.4640007 3.17700005 15.95699978 N +37 1 C 21.88800049 4.23600006 15.15699959 C-Alpha +38 1 C 20.43600082 3.91000009 14.75199986 C-Prime +39 1 O 19.68499947 4.89900017 14.97099972 O +40 1 C 22.6989994 4.64599991 13.93500042 C-Beta +41 1 N 20.07500076 2.72799993 14.35099983 N +42 1 C 18.73999977 2.273 14.02000046 C-Alpha +43 1 C 17.80699921 2.36500001 15.17700005 C-Prime +44 1 O 16.64800072 2.89899993 15.09599972 O +45 1 C 18.7329998 0.86000001 13.41800022 C-Beta diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2.in b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2.in new file mode 100644 index 00000000..803261f2 --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2.in @@ -0,0 +1,52 @@ +# 3d protein simulation + +units real + +timestep 2 + +dimension 3 + +boundary s s s +#boundary p p p + +neighbor 10 bin +neigh_modify delay 5 + +atom_modify sort 0 0.0 + +special_bonds fene + +atom_style awsemmd + +bond_style harmonic + +pair_style vexcluded 2 3.5 3.5 + +read_data data.2mlt_frag2 + +pair_coeff * * 0.0 +pair_coeff 1 1 20.0 3.5 4.5 +pair_coeff 1 4 20.0 3.5 4.5 +pair_coeff 4 4 20.0 3.5 4.5 +pair_coeff 3 3 20.0 3.5 3.5 + + +velocity all create 300.0 2349852 + +group alpha_carbons id 1 4 7 10 13 16 19 22 25 + +group beta_atoms id 3 6 9 12 15 18 21 24 27 + +group oxygens id 2 5 8 11 14 17 20 23 26 + + +fix 1 all nvt temp 300.0 300.0 100.0 +fix 2 alpha_carbons backbone beta_atoms oxygens fix_backbone_coeff.data 2mlt_frag2.seq + +thermo 1000 +dump 1 all atom 1000 dump.lammpstrj + +dump_modify 1 sort id + +reset_timestep 0 +run 0 diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2.pdb b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2.pdb new file mode 100644 index 00000000..6673da8e --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2.pdb @@ -0,0 +1,87 @@ +CRYST1 60.832 38.293 42.211 90.00 90.00 90.00 C 2 2 21 16 +ORIGX1 1.000000 0.000000 0.000000 0.00000 +ORIGX2 0.000000 1.000000 0.000000 0.00000 +ORIGX3 0.000000 0.000000 1.000000 0.00000 +SCALE1 0.016439 0.000000 0.000000 0.00000 +SCALE2 0.000000 0.026114 0.000000 0.00000 +SCALE3 0.000000 0.000000 0.023691 0.00000 +MTRIX1 1 -0.996310 -0.033870 -0.078870 71.25100 1 +MTRIX2 1 0.048050 -0.981470 -0.185470 2.71100 1 +MTRIX3 1 -0.071130 -0.188580 0.979480 2.05300 1 +ATOM 87 N PRO A 14 31.689 -1.979 14.106 1.00 17.38 N +ATOM 88 CA PRO A 14 31.026 -1.278 13.030 1.00 17.52 C +ATOM 89 C PRO A 14 29.521 -1.670 12.857 1.00 18.98 C +ATOM 90 O PRO A 14 28.657 -0.801 12.744 1.00 16.75 O +ATOM 91 CB PRO A 14 31.845 -1.614 11.816 1.00 17.80 C +ATOM 92 CG PRO A 14 33.118 -2.205 12.303 1.00 18.05 C +ATOM 93 CD PRO A 14 33.098 -2.363 13.769 1.00 17.96 C +ATOM 94 N ALA A 15 29.207 -2.952 12.868 1.00 16.39 N +ATOM 95 CA ALA A 15 27.822 -3.418 12.724 1.00 17.10 C +ATOM 96 C ALA A 15 27.023 -3.016 13.951 1.00 16.98 C +ATOM 97 O ALA A 15 25.872 -2.551 13.769 1.00 16.78 O +ATOM 98 CB ALA A 15 27.741 -4.906 12.502 1.00 19.58 C +ATOM 99 N LEU A 16 27.570 -3.117 15.127 1.00 15.97 N +ATOM 100 CA LEU A 16 26.958 -2.649 16.351 1.00 18.20 C +ATOM 101 C LEU A 16 26.614 -1.169 16.344 1.00 20.28 C +ATOM 102 O LEU A 16 25.599 -0.734 16.933 1.00 18.32 O +ATOM 103 CB LEU A 16 27.811 -3.027 17.542 1.00 19.70 C +ATOM 104 CG LEU A 16 27.384 -2.550 18.921 1.00 22.23 C +ATOM 105 CD1 LEU A 16 26.031 -3.234 19.257 1.00 27.80 C +ATOM 106 CD2 LEU A 16 28.445 -2.970 19.933 1.00 21.91 C +ATOM 107 N ILE A 17 27.514 -0.365 15.791 1.00 20.97 N +ATOM 108 CA ILE A 17 27.343 1.056 15.618 1.00 20.41 C +ATOM 109 C ILE A 17 26.081 1.392 14.758 1.00 18.17 C +ATOM 110 O ILE A 17 25.380 2.240 15.282 1.00 16.46 O +ATOM 111 CB ILE A 17 28.579 1.847 15.132 1.00 21.10 C +ATOM 112 CG1 ILE A 17 29.586 1.858 16.352 1.00 25.66 C +ATOM 113 CG2 ILE A 17 28.268 3.288 14.691 1.00 22.04 C +ATOM 114 CD1 ILE A 17 30.856 2.696 16.161 1.00 27.00 C +ATOM 115 N SER A 18 25.930 0.759 13.657 1.00 16.97 N +ATOM 116 CA SER A 18 24.825 0.827 12.744 1.00 19.98 C +ATOM 117 C SER A 18 23.499 0.405 13.438 1.00 18.89 C +ATOM 118 O SER A 18 22.557 1.165 13.352 1.00 18.37 O +ATOM 119 CB SER A 18 25.076 0.039 11.491 1.00 20.39 C +ATOM 120 OG SER A 18 23.902 0.046 10.670 1.00 23.87 O +ATOM 121 N TRP A 19 23.512 -0.661 14.161 1.00 17.71 N +ATOM 122 CA TRP A 19 22.492 -1.085 15.081 1.00 15.72 C +ATOM 123 C TRP A 19 22.083 0.004 16.012 1.00 18.02 C +ATOM 124 O TRP A 19 20.820 0.244 16.160 1.00 16.93 O +ATOM 125 CB TRP A 19 22.854 -2.410 15.767 1.00 15.59 C +ATOM 126 CG TRP A 19 21.803 -2.993 16.678 1.00 17.94 C +ATOM 127 CD1 TRP A 19 20.917 -3.950 16.210 1.00 18.03 C +ATOM 128 CD2 TRP A 19 21.448 -2.745 18.041 1.00 16.03 C +ATOM 129 NE1 TRP A 19 20.060 -4.304 17.222 1.00 21.28 N +ATOM 130 CE2 TRP A 19 20.357 -3.624 18.372 1.00 20.45 C +ATOM 131 CE3 TRP A 19 21.879 -1.892 19.048 1.00 14.41 C +ATOM 132 CZ2 TRP A 19 19.784 -3.690 19.612 1.00 17.15 C +ATOM 133 CZ3 TRP A 19 21.292 -1.950 20.288 1.00 17.24 C +ATOM 134 CH2 TRP A 19 20.230 -2.805 20.601 1.00 15.13 C +ATOM 135 N ILE A 20 22.930 0.594 16.823 1.00 14.82 N +ATOM 136 CA ILE A 20 22.628 1.633 17.766 1.00 15.67 C +ATOM 137 C ILE A 20 21.917 2.819 17.080 1.00 17.51 C +ATOM 138 O ILE A 20 20.942 3.365 17.655 1.00 17.70 O +ATOM 139 CB ILE A 20 23.902 2.192 18.499 1.00 16.25 C +ATOM 140 CG1 ILE A 20 24.481 0.986 19.363 1.00 15.50 C +ATOM 141 CG2 ILE A 20 23.599 3.421 19.390 1.00 14.54 C +ATOM 142 CD1 ILE A 20 26.033 1.304 19.637 1.00 18.18 C +ATOM 143 N LYS A 21 22.464 3.177 15.957 1.00 16.61 N +ATOM 144 CA LYS A 21 21.888 4.236 15.157 1.00 19.84 C +ATOM 145 C LYS A 21 20.436 3.910 14.752 1.00 21.02 C +ATOM 146 O LYS A 21 19.685 4.899 14.971 1.00 22.80 O +ATOM 147 CB LYS A 21 22.699 4.646 13.935 1.00 16.73 C +ATOM 148 CG LYS A 21 23.944 5.416 14.471 1.00 22.19 C +ATOM 149 CD LYS A 21 24.919 5.669 13.300 1.00 25.86 C +ATOM 150 CE LYS A 21 26.173 6.287 13.908 1.00 32.91 C +ATOM 151 NZ LYS A 21 27.199 6.564 12.863 1.00 39.11 N +ATOM 152 N ARG A 22 20.075 2.728 14.351 1.00 19.18 N +ATOM 153 CA ARG A 22 18.740 2.273 14.020 1.00 20.38 C +ATOM 154 C ARG A 22 17.807 2.365 15.177 1.00 22.46 C +ATOM 155 O ARG A 22 16.648 2.899 15.096 1.00 23.24 O +ATOM 156 CB ARG A 22 18.733 0.860 13.418 1.00 22.73 C +ATOM 157 CG ARG A 22 19.309 0.956 12.004 1.00 22.29 C +ATOM 158 CD ARG A 22 19.117 -0.300 11.254 1.00 25.78 C +ATOM 159 NE ARG A 22 19.382 -1.562 11.991 1.00 28.94 N +ATOM 160 CZ ARG A 22 20.624 -2.104 11.889 1.00 33.77 C +ATOM 161 NH1 ARG A 22 21.664 -1.554 11.252 1.00 31.21 N +ATOM 162 NH2 ARG A 22 20.870 -3.271 12.498 1.00 33.11 N +END diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2.seq b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2.seq new file mode 100644 index 00000000..2193ce31 --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2.seq @@ -0,0 +1 @@ +PALISWIKR diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2/2mlt_frag2-cleaned.pdb b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2/2mlt_frag2-cleaned.pdb new file mode 100644 index 00000000..b1f527a9 --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2/2mlt_frag2-cleaned.pdb @@ -0,0 +1,169 @@ +REMARK 1 CREATED WITH OPENMM 8.1.1, 2025-12-23 +CRYST1 60.832 38.293 42.211 90.00 90.00 90.00 P 1 1 +ATOM 1 N PRO A 14 31.689 -1.979 14.106 1.00 0.00 N +ATOM 2 H2 PRO A 14 31.276 -2.955 14.661 1.00 0.00 H +ATOM 3 H3 PRO A 14 31.802 -1.230 15.035 1.00 0.00 H +ATOM 4 CA PRO A 14 31.026 -1.278 13.030 1.00 0.00 C +ATOM 5 HA PRO A 14 31.087 -0.087 13.067 1.00 0.00 H +ATOM 6 C PRO A 14 29.521 -1.670 12.857 1.00 0.00 C +ATOM 7 O PRO A 14 28.657 -0.801 12.744 1.00 0.00 O +ATOM 8 CB PRO A 14 31.845 -1.614 11.816 1.00 0.00 C +ATOM 9 HB2 PRO A 14 31.360 -2.281 10.948 1.00 0.00 H +ATOM 10 HB3 PRO A 14 32.105 -0.652 11.150 1.00 0.00 H +ATOM 11 CG PRO A 14 33.118 -2.205 12.303 1.00 0.00 C +ATOM 12 HG2 PRO A 14 33.354 -3.243 11.750 1.00 0.00 H +ATOM 13 HG3 PRO A 14 34.080 -1.569 11.972 1.00 0.00 H +ATOM 14 CD PRO A 14 33.098 -2.363 13.769 1.00 0.00 C +ATOM 15 HD2 PRO A 14 33.941 -1.705 14.312 1.00 0.00 H +ATOM 16 HD3 PRO A 14 33.456 -3.462 14.092 1.00 0.00 H +ATOM 17 N ALA A 15 29.207 -2.952 12.868 1.00 0.00 N +ATOM 18 H ALA A 15 30.005 -3.794 12.606 1.00 0.00 H +ATOM 19 CA ALA A 15 27.822 -3.418 12.724 1.00 0.00 C +ATOM 20 HA ALA A 15 27.464 -2.944 11.690 1.00 0.00 H +ATOM 21 C ALA A 15 27.023 -3.016 13.951 1.00 0.00 C +ATOM 22 O ALA A 15 25.872 -2.551 13.769 1.00 0.00 O +ATOM 23 CB ALA A 15 27.741 -4.906 12.502 1.00 0.00 C +ATOM 24 HB1 ALA A 15 26.960 -5.122 11.612 1.00 0.00 H +ATOM 25 HB2 ALA A 15 27.299 -5.602 13.372 1.00 0.00 H +ATOM 26 HB3 ALA A 15 28.660 -5.560 12.095 1.00 0.00 H +ATOM 27 N LEU A 16 27.570 -3.117 15.127 1.00 0.00 N +ATOM 28 H LEU A 16 28.311 -4.043 15.235 1.00 0.00 H +ATOM 29 CA LEU A 16 26.958 -2.649 16.351 1.00 0.00 C +ATOM 30 HA LEU A 16 26.042 -3.413 16.370 1.00 0.00 H +ATOM 31 C LEU A 16 26.614 -1.169 16.344 1.00 0.00 C +ATOM 32 O LEU A 16 25.599 -0.734 16.933 1.00 0.00 O +ATOM 33 CB LEU A 16 27.811 -3.027 17.542 1.00 0.00 C +ATOM 34 HB2 LEU A 16 28.937 -2.668 17.356 1.00 0.00 H +ATOM 35 HB3 LEU A 16 27.935 -4.219 17.610 1.00 0.00 H +ATOM 36 CG LEU A 16 27.384 -2.550 18.921 1.00 0.00 C +ATOM 37 HG LEU A 16 27.514 -1.374 19.018 1.00 0.00 H +ATOM 38 CD1 LEU A 16 26.031 -3.234 19.257 1.00 0.00 C +ATOM 39 HD11 LEU A 16 24.991 -2.840 18.834 1.00 0.00 H +ATOM 40 HD12 LEU A 16 25.864 -3.158 20.443 1.00 0.00 H +ATOM 41 HD13 LEU A 16 25.963 -4.423 19.106 1.00 0.00 H +ATOM 42 CD2 LEU A 16 28.445 -2.970 19.933 1.00 0.00 C +ATOM 43 HD21 LEU A 16 28.316 -4.043 20.454 1.00 0.00 H +ATOM 44 HD22 LEU A 16 29.611 -3.035 19.656 1.00 0.00 H +ATOM 45 HD23 LEU A 16 28.497 -2.237 20.881 1.00 0.00 H +ATOM 46 N ILE A 17 27.514 -0.365 15.791 1.00 0.00 N +ATOM 47 H ILE A 17 28.628 -0.758 15.698 1.00 0.00 H +ATOM 48 CA ILE A 17 27.343 1.056 15.618 1.00 0.00 C +ATOM 49 HA ILE A 17 27.131 1.458 16.719 1.00 0.00 H +ATOM 50 C ILE A 17 26.081 1.392 14.758 1.00 0.00 C +ATOM 51 O ILE A 17 25.380 2.240 15.282 1.00 0.00 O +ATOM 52 CB ILE A 17 28.579 1.847 15.132 1.00 0.00 C +ATOM 53 HB ILE A 17 29.228 1.447 14.218 1.00 0.00 H +ATOM 54 CG1 ILE A 17 29.586 1.858 16.352 1.00 0.00 C +ATOM 55 HG12 ILE A 17 29.162 2.458 17.298 1.00 0.00 H +ATOM 56 HG13 ILE A 17 30.039 0.835 16.791 1.00 0.00 H +ATOM 57 CG2 ILE A 17 28.268 3.288 14.691 1.00 0.00 C +ATOM 58 HG21 ILE A 17 28.042 3.268 13.517 1.00 0.00 H +ATOM 59 HG22 ILE A 17 29.137 4.118 14.665 1.00 0.00 H +ATOM 60 HG23 ILE A 17 27.512 3.793 15.466 1.00 0.00 H +ATOM 61 CD1 ILE A 17 30.856 2.696 16.161 1.00 0.00 C +ATOM 62 HD11 ILE A 17 31.458 2.727 17.204 1.00 0.00 H +ATOM 63 HD12 ILE A 17 31.660 2.198 15.423 1.00 0.00 H +ATOM 64 HD13 ILE A 17 30.974 3.856 15.882 1.00 0.00 H +ATOM 65 N SER A 18 25.930 0.759 13.657 1.00 0.00 N +ATOM 66 H SER A 18 26.912 0.800 12.987 1.00 0.00 H +ATOM 67 CA SER A 18 24.825 0.827 12.744 1.00 0.00 C +ATOM 68 HA SER A 18 24.692 1.936 12.326 1.00 0.00 H +ATOM 69 C SER A 18 23.499 0.405 13.438 1.00 0.00 C +ATOM 70 O SER A 18 22.557 1.165 13.352 1.00 0.00 O +ATOM 71 CB SER A 18 25.076 0.039 11.491 1.00 0.00 C +ATOM 72 HB2 SER A 18 25.292 -1.128 11.323 1.00 0.00 H +ATOM 73 HB3 SER A 18 25.948 0.476 10.797 1.00 0.00 H +ATOM 74 OG SER A 18 23.902 0.046 10.670 1.00 0.00 O +ATOM 75 HG SER A 18 24.014 0.879 9.826 1.00 0.00 H +ATOM 76 N TRP A 19 23.512 -0.661 14.161 1.00 0.00 N +ATOM 77 H TRP A 19 24.036 -1.593 13.643 1.00 0.00 H +ATOM 78 CA TRP A 19 22.492 -1.085 15.081 1.00 0.00 C +ATOM 79 HA TRP A 19 21.482 -1.368 14.518 1.00 0.00 H +ATOM 80 C TRP A 19 22.083 0.004 16.012 1.00 0.00 C +ATOM 81 O TRP A 19 20.820 0.244 16.160 1.00 0.00 O +ATOM 82 CB TRP A 19 22.854 -2.410 15.767 1.00 0.00 C +ATOM 83 HB2 TRP A 19 23.060 -3.306 15.000 1.00 0.00 H +ATOM 84 HB3 TRP A 19 23.734 -2.485 16.561 1.00 0.00 H +ATOM 85 CG TRP A 19 21.803 -2.993 16.678 1.00 0.00 C +ATOM 86 CD1 TRP A 19 20.917 -3.950 16.210 1.00 0.00 C +ATOM 87 HD1 TRP A 19 21.162 -4.946 15.606 1.00 0.00 H +ATOM 88 CD2 TRP A 19 21.448 -2.745 18.041 1.00 0.00 C +ATOM 89 NE1 TRP A 19 20.060 -4.304 17.222 1.00 0.00 N +ATOM 90 HE1 TRP A 19 19.166 -5.082 17.130 1.00 0.00 H +ATOM 91 CE2 TRP A 19 20.357 -3.624 18.372 1.00 0.00 C +ATOM 92 CE3 TRP A 19 21.879 -1.892 19.048 1.00 0.00 C +ATOM 93 HE3 TRP A 19 23.012 -1.653 19.280 1.00 0.00 H +ATOM 94 CZ2 TRP A 19 19.784 -3.690 19.612 1.00 0.00 C +ATOM 95 HZ2 TRP A 19 18.893 -4.428 19.882 1.00 0.00 H +ATOM 96 CZ3 TRP A 19 21.292 -1.950 20.288 1.00 0.00 C +ATOM 97 HZ3 TRP A 19 21.593 -1.341 21.264 1.00 0.00 H +ATOM 98 CH2 TRP A 19 20.230 -2.805 20.601 1.00 0.00 C +ATOM 99 HH2 TRP A 19 19.699 -2.847 21.664 1.00 0.00 H +ATOM 100 N ILE A 20 22.930 0.594 16.823 1.00 0.00 N +ATOM 101 H ILE A 20 24.076 0.541 16.550 1.00 0.00 H +ATOM 102 CA ILE A 20 22.628 1.633 17.766 1.00 0.00 C +ATOM 103 HA ILE A 20 21.789 1.290 18.542 1.00 0.00 H +ATOM 104 C ILE A 20 21.917 2.819 17.080 1.00 0.00 C +ATOM 105 O ILE A 20 20.942 3.365 17.655 1.00 0.00 O +ATOM 106 CB ILE A 20 23.902 2.192 18.499 1.00 0.00 C +ATOM 107 HB ILE A 20 24.715 2.724 17.819 1.00 0.00 H +ATOM 108 CG1 ILE A 20 24.481 0.986 19.363 1.00 0.00 C +ATOM 109 HG12 ILE A 20 23.788 1.030 20.353 1.00 0.00 H +ATOM 110 HG13 ILE A 20 24.628 -0.201 19.461 1.00 0.00 H +ATOM 111 CG2 ILE A 20 23.599 3.421 19.390 1.00 0.00 C +ATOM 112 HG21 ILE A 20 22.661 3.366 20.137 1.00 0.00 H +ATOM 113 HG22 ILE A 20 23.360 4.447 18.810 1.00 0.00 H +ATOM 114 HG23 ILE A 20 24.460 3.891 20.098 1.00 0.00 H +ATOM 115 CD1 ILE A 20 26.033 1.304 19.637 1.00 0.00 C +ATOM 116 HD11 ILE A 20 26.619 2.239 19.171 1.00 0.00 H +ATOM 117 HD12 ILE A 20 26.965 0.585 19.850 1.00 0.00 H +ATOM 118 HD13 ILE A 20 25.915 1.670 20.777 1.00 0.00 H +ATOM 119 N LYS A 21 22.464 3.177 15.957 1.00 0.00 N +ATOM 120 H LYS A 21 23.548 2.990 15.537 1.00 0.00 H +ATOM 121 CA LYS A 21 21.888 4.236 15.157 1.00 0.00 C +ATOM 122 HA LYS A 21 21.684 5.156 15.887 1.00 0.00 H +ATOM 123 C LYS A 21 20.436 3.910 14.752 1.00 0.00 C +ATOM 124 O LYS A 21 19.685 4.899 14.971 1.00 0.00 O +ATOM 125 CB LYS A 21 22.699 4.646 13.935 1.00 0.00 C +ATOM 126 HB2 LYS A 21 21.993 5.432 13.366 1.00 0.00 H +ATOM 127 HB3 LYS A 21 22.859 3.879 13.036 1.00 0.00 H +ATOM 128 CG LYS A 21 23.944 5.416 14.471 1.00 0.00 C +ATOM 129 HG2 LYS A 21 23.539 6.515 14.726 1.00 0.00 H +ATOM 130 HG3 LYS A 21 24.475 5.169 15.505 1.00 0.00 H +ATOM 131 CD LYS A 21 24.919 5.669 13.300 1.00 0.00 C +ATOM 132 HD2 LYS A 21 24.419 6.421 12.513 1.00 0.00 H +ATOM 133 HD3 LYS A 21 25.267 4.750 12.623 1.00 0.00 H +ATOM 134 CE LYS A 21 26.173 6.287 13.908 1.00 0.00 C +ATOM 135 HE2 LYS A 21 25.834 7.406 14.184 1.00 0.00 H +ATOM 136 HE3 LYS A 21 26.807 6.035 14.888 1.00 0.00 H +ATOM 137 NZ LYS A 21 27.199 6.564 12.863 1.00 0.00 N +ATOM 138 HZ1 LYS A 21 26.833 7.125 11.866 1.00 0.00 H +ATOM 139 HZ2 LYS A 21 27.890 5.710 12.384 1.00 0.00 H +ATOM 140 HZ3 LYS A 21 28.009 7.353 13.267 1.00 0.00 H +ATOM 141 N ARG A 22 20.075 2.728 14.351 1.00 0.00 N +ATOM 142 H ARG A 22 20.875 1.866 14.278 1.00 0.00 H +ATOM 143 CA ARG A 22 18.740 2.273 14.020 1.00 0.00 C +ATOM 144 HA ARG A 22 18.281 3.145 13.343 1.00 0.00 H +ATOM 145 C ARG A 22 17.807 2.365 15.177 1.00 0.00 C +ATOM 146 O ARG A 22 16.648 2.899 15.096 1.00 0.00 O +ATOM 147 CB ARG A 22 18.733 0.860 13.418 1.00 0.00 C +ATOM 148 HB2 ARG A 22 18.954 -0.058 14.146 1.00 0.00 H +ATOM 149 HB3 ARG A 22 17.556 0.698 13.252 1.00 0.00 H +ATOM 150 CG ARG A 22 19.309 0.956 12.004 1.00 0.00 C +ATOM 151 HG2 ARG A 22 18.649 1.739 11.375 1.00 0.00 H +ATOM 152 HG3 ARG A 22 20.397 1.373 11.744 1.00 0.00 H +ATOM 153 CD ARG A 22 19.117 -0.300 11.254 1.00 0.00 C +ATOM 154 HD2 ARG A 22 19.518 -0.186 10.130 1.00 0.00 H +ATOM 155 HD3 ARG A 22 17.968 -0.467 10.943 1.00 0.00 H +ATOM 156 NE ARG A 22 19.382 -1.562 11.991 1.00 0.00 N +ATOM 157 HE ARG A 22 18.475 -2.310 12.190 1.00 0.00 H +ATOM 158 CZ ARG A 22 20.624 -2.104 11.889 1.00 0.00 C +ATOM 159 NH1 ARG A 22 21.664 -1.554 11.252 1.00 0.00 N +ATOM 160 HH11 ARG A 22 21.542 -1.383 10.077 1.00 0.00 H +ATOM 161 HH12 ARG A 22 22.689 -2.158 11.323 1.00 0.00 H +ATOM 162 NH2 ARG A 22 20.870 -3.271 12.498 1.00 0.00 N +ATOM 163 HH21 ARG A 22 20.997 -4.155 11.703 1.00 0.00 H +ATOM 164 HH22 ARG A 22 20.378 -3.797 13.442 1.00 0.00 H +ATOM 165 OXT ARG A 22 18.610 1.777 15.932 1.00 0.00 O +TER 166 ARG A 22 +END diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2/2mlt_frag2-openmmawsem.pdb b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2/2mlt_frag2-openmmawsem.pdb new file mode 100644 index 00000000..3c4c0e1a --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2/2mlt_frag2-openmmawsem.pdb @@ -0,0 +1,53 @@ +ATOM 1 CA IPR A 14 31.026 -1.278 13.030 1.00 0.00 C +ATOM 2 C IPR A 14 29.512 -1.628 12.866 1.00 0.00 C +ATOM 3 O IPR A 14 28.657 -0.801 12.744 1.00 0.00 O +ATOM 4 CB IPR A 14 31.845 -1.614 11.816 1.00 0.00 B +ATOM 5 N NGP A 15 29.215 -2.872 12.869 1.00 0.00 N +ATOM 6 H NGP A 15 29.906 -3.539 12.968 1.00 0.00 H +ATOM 7 CA NGP A 15 27.822 -3.418 12.724 1.00 0.00 C +ATOM 8 C NGP A 15 26.993 -2.959 13.913 1.00 0.00 C +ATOM 9 O NGP A 15 25.872 -2.551 13.769 1.00 0.00 O +ATOM 10 CB NGP A 15 27.741 -4.906 12.502 1.00 0.00 B +ATOM 11 N NGP A 16 27.579 -3.039 15.080 1.00 0.00 N +ATOM 12 H NGP A 16 28.484 -3.368 15.197 1.00 0.00 H +ATOM 13 CA NGP A 16 26.958 -2.649 16.351 1.00 0.00 C +ATOM 14 C NGP A 16 26.612 -1.163 16.366 1.00 0.00 C +ATOM 15 O NGP A 16 25.599 -0.734 16.933 1.00 0.00 O +ATOM 16 CB NGP A 16 27.811 -3.027 17.542 1.00 0.00 B +ATOM 17 N NGP A 17 27.483 -0.400 15.727 1.00 0.00 N +ATOM 18 H NGP A 17 28.301 -0.746 15.270 1.00 0.00 H +ATOM 19 CA NGP A 17 27.343 1.056 15.618 1.00 0.00 C +ATOM 20 C NGP A 17 26.120 1.382 14.834 1.00 0.00 C +ATOM 21 O NGP A 17 25.380 2.240 15.282 1.00 0.00 O +ATOM 22 CB NGP A 17 28.579 1.847 15.132 1.00 0.00 B +ATOM 23 N NGP A 18 25.939 0.674 13.660 1.00 0.00 N +ATOM 24 H NGP A 18 26.537 -0.017 13.299 1.00 0.00 H +ATOM 25 CA NGP A 18 24.825 0.827 12.744 1.00 0.00 C +ATOM 26 C NGP A 18 23.548 0.486 13.489 1.00 0.00 C +ATOM 27 O NGP A 18 22.557 1.165 13.352 1.00 0.00 O +ATOM 28 CB NGP A 18 25.076 0.039 11.491 1.00 0.00 B +ATOM 29 N NGP A 19 23.608 -0.581 14.275 1.00 0.00 N +ATOM 30 H NGP A 19 24.408 -1.128 14.386 1.00 0.00 H +ATOM 31 CA NGP A 19 22.492 -1.085 15.081 1.00 0.00 C +ATOM 32 C NGP A 19 21.987 -0.019 16.059 1.00 0.00 C +ATOM 33 O NGP A 19 20.820 0.244 16.160 1.00 0.00 O +ATOM 34 CB NGP A 19 22.854 -2.410 15.767 1.00 0.00 B +ATOM 35 N NGP A 20 22.900 0.579 16.769 1.00 0.00 N +ATOM 36 H NGP A 20 23.842 0.367 16.688 1.00 0.00 H +ATOM 37 CA NGP A 20 22.628 1.633 17.766 1.00 0.00 C +ATOM 38 C NGP A 20 21.912 2.801 17.117 1.00 0.00 C +ATOM 39 O NGP A 20 20.942 3.365 17.655 1.00 0.00 O +ATOM 40 CB NGP A 20 23.902 2.192 18.499 1.00 0.00 B +ATOM 41 N NGP A 21 22.423 3.141 15.952 1.00 0.00 N +ATOM 42 H NGP A 21 23.206 2.686 15.519 1.00 0.00 H +ATOM 43 CA NGP A 21 21.888 4.236 15.157 1.00 0.00 C +ATOM 44 C NGP A 21 20.440 3.987 14.830 1.00 0.00 C +ATOM 45 O NGP A 21 19.685 4.899 14.971 1.00 0.00 O +ATOM 46 CB NGP A 21 22.699 4.646 13.935 1.00 0.00 B +ATOM 47 N NGP A 22 20.085 2.732 14.393 1.00 0.00 N +ATOM 48 H NGP A 22 20.695 1.997 14.279 1.00 0.00 H +ATOM 49 CA NGP A 22 18.740 2.273 14.020 1.00 0.00 C +ATOM 50 O NGP A 22 16.648 2.899 15.096 1.00 0.00 O +ATOM 51 CB NGP A 22 18.733 0.860 13.418 1.00 0.00 B +TER 52 CB NGP A 22 +END diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2/2mlt_frag2.fasta b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2/2mlt_frag2.fasta new file mode 100644 index 00000000..ecad78e0 --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2/2mlt_frag2.fasta @@ -0,0 +1,2 @@ +>CRYSTAL_STRUCTURE:A +PALISWIKR diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2/2mlt_frag2.pdb b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2/2mlt_frag2.pdb new file mode 100644 index 00000000..b1f527a9 --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2/2mlt_frag2.pdb @@ -0,0 +1,169 @@ +REMARK 1 CREATED WITH OPENMM 8.1.1, 2025-12-23 +CRYST1 60.832 38.293 42.211 90.00 90.00 90.00 P 1 1 +ATOM 1 N PRO A 14 31.689 -1.979 14.106 1.00 0.00 N +ATOM 2 H2 PRO A 14 31.276 -2.955 14.661 1.00 0.00 H +ATOM 3 H3 PRO A 14 31.802 -1.230 15.035 1.00 0.00 H +ATOM 4 CA PRO A 14 31.026 -1.278 13.030 1.00 0.00 C +ATOM 5 HA PRO A 14 31.087 -0.087 13.067 1.00 0.00 H +ATOM 6 C PRO A 14 29.521 -1.670 12.857 1.00 0.00 C +ATOM 7 O PRO A 14 28.657 -0.801 12.744 1.00 0.00 O +ATOM 8 CB PRO A 14 31.845 -1.614 11.816 1.00 0.00 C +ATOM 9 HB2 PRO A 14 31.360 -2.281 10.948 1.00 0.00 H +ATOM 10 HB3 PRO A 14 32.105 -0.652 11.150 1.00 0.00 H +ATOM 11 CG PRO A 14 33.118 -2.205 12.303 1.00 0.00 C +ATOM 12 HG2 PRO A 14 33.354 -3.243 11.750 1.00 0.00 H +ATOM 13 HG3 PRO A 14 34.080 -1.569 11.972 1.00 0.00 H +ATOM 14 CD PRO A 14 33.098 -2.363 13.769 1.00 0.00 C +ATOM 15 HD2 PRO A 14 33.941 -1.705 14.312 1.00 0.00 H +ATOM 16 HD3 PRO A 14 33.456 -3.462 14.092 1.00 0.00 H +ATOM 17 N ALA A 15 29.207 -2.952 12.868 1.00 0.00 N +ATOM 18 H ALA A 15 30.005 -3.794 12.606 1.00 0.00 H +ATOM 19 CA ALA A 15 27.822 -3.418 12.724 1.00 0.00 C +ATOM 20 HA ALA A 15 27.464 -2.944 11.690 1.00 0.00 H +ATOM 21 C ALA A 15 27.023 -3.016 13.951 1.00 0.00 C +ATOM 22 O ALA A 15 25.872 -2.551 13.769 1.00 0.00 O +ATOM 23 CB ALA A 15 27.741 -4.906 12.502 1.00 0.00 C +ATOM 24 HB1 ALA A 15 26.960 -5.122 11.612 1.00 0.00 H +ATOM 25 HB2 ALA A 15 27.299 -5.602 13.372 1.00 0.00 H +ATOM 26 HB3 ALA A 15 28.660 -5.560 12.095 1.00 0.00 H +ATOM 27 N LEU A 16 27.570 -3.117 15.127 1.00 0.00 N +ATOM 28 H LEU A 16 28.311 -4.043 15.235 1.00 0.00 H +ATOM 29 CA LEU A 16 26.958 -2.649 16.351 1.00 0.00 C +ATOM 30 HA LEU A 16 26.042 -3.413 16.370 1.00 0.00 H +ATOM 31 C LEU A 16 26.614 -1.169 16.344 1.00 0.00 C +ATOM 32 O LEU A 16 25.599 -0.734 16.933 1.00 0.00 O +ATOM 33 CB LEU A 16 27.811 -3.027 17.542 1.00 0.00 C +ATOM 34 HB2 LEU A 16 28.937 -2.668 17.356 1.00 0.00 H +ATOM 35 HB3 LEU A 16 27.935 -4.219 17.610 1.00 0.00 H +ATOM 36 CG LEU A 16 27.384 -2.550 18.921 1.00 0.00 C +ATOM 37 HG LEU A 16 27.514 -1.374 19.018 1.00 0.00 H +ATOM 38 CD1 LEU A 16 26.031 -3.234 19.257 1.00 0.00 C +ATOM 39 HD11 LEU A 16 24.991 -2.840 18.834 1.00 0.00 H +ATOM 40 HD12 LEU A 16 25.864 -3.158 20.443 1.00 0.00 H +ATOM 41 HD13 LEU A 16 25.963 -4.423 19.106 1.00 0.00 H +ATOM 42 CD2 LEU A 16 28.445 -2.970 19.933 1.00 0.00 C +ATOM 43 HD21 LEU A 16 28.316 -4.043 20.454 1.00 0.00 H +ATOM 44 HD22 LEU A 16 29.611 -3.035 19.656 1.00 0.00 H +ATOM 45 HD23 LEU A 16 28.497 -2.237 20.881 1.00 0.00 H +ATOM 46 N ILE A 17 27.514 -0.365 15.791 1.00 0.00 N +ATOM 47 H ILE A 17 28.628 -0.758 15.698 1.00 0.00 H +ATOM 48 CA ILE A 17 27.343 1.056 15.618 1.00 0.00 C +ATOM 49 HA ILE A 17 27.131 1.458 16.719 1.00 0.00 H +ATOM 50 C ILE A 17 26.081 1.392 14.758 1.00 0.00 C +ATOM 51 O ILE A 17 25.380 2.240 15.282 1.00 0.00 O +ATOM 52 CB ILE A 17 28.579 1.847 15.132 1.00 0.00 C +ATOM 53 HB ILE A 17 29.228 1.447 14.218 1.00 0.00 H +ATOM 54 CG1 ILE A 17 29.586 1.858 16.352 1.00 0.00 C +ATOM 55 HG12 ILE A 17 29.162 2.458 17.298 1.00 0.00 H +ATOM 56 HG13 ILE A 17 30.039 0.835 16.791 1.00 0.00 H +ATOM 57 CG2 ILE A 17 28.268 3.288 14.691 1.00 0.00 C +ATOM 58 HG21 ILE A 17 28.042 3.268 13.517 1.00 0.00 H +ATOM 59 HG22 ILE A 17 29.137 4.118 14.665 1.00 0.00 H +ATOM 60 HG23 ILE A 17 27.512 3.793 15.466 1.00 0.00 H +ATOM 61 CD1 ILE A 17 30.856 2.696 16.161 1.00 0.00 C +ATOM 62 HD11 ILE A 17 31.458 2.727 17.204 1.00 0.00 H +ATOM 63 HD12 ILE A 17 31.660 2.198 15.423 1.00 0.00 H +ATOM 64 HD13 ILE A 17 30.974 3.856 15.882 1.00 0.00 H +ATOM 65 N SER A 18 25.930 0.759 13.657 1.00 0.00 N +ATOM 66 H SER A 18 26.912 0.800 12.987 1.00 0.00 H +ATOM 67 CA SER A 18 24.825 0.827 12.744 1.00 0.00 C +ATOM 68 HA SER A 18 24.692 1.936 12.326 1.00 0.00 H +ATOM 69 C SER A 18 23.499 0.405 13.438 1.00 0.00 C +ATOM 70 O SER A 18 22.557 1.165 13.352 1.00 0.00 O +ATOM 71 CB SER A 18 25.076 0.039 11.491 1.00 0.00 C +ATOM 72 HB2 SER A 18 25.292 -1.128 11.323 1.00 0.00 H +ATOM 73 HB3 SER A 18 25.948 0.476 10.797 1.00 0.00 H +ATOM 74 OG SER A 18 23.902 0.046 10.670 1.00 0.00 O +ATOM 75 HG SER A 18 24.014 0.879 9.826 1.00 0.00 H +ATOM 76 N TRP A 19 23.512 -0.661 14.161 1.00 0.00 N +ATOM 77 H TRP A 19 24.036 -1.593 13.643 1.00 0.00 H +ATOM 78 CA TRP A 19 22.492 -1.085 15.081 1.00 0.00 C +ATOM 79 HA TRP A 19 21.482 -1.368 14.518 1.00 0.00 H +ATOM 80 C TRP A 19 22.083 0.004 16.012 1.00 0.00 C +ATOM 81 O TRP A 19 20.820 0.244 16.160 1.00 0.00 O +ATOM 82 CB TRP A 19 22.854 -2.410 15.767 1.00 0.00 C +ATOM 83 HB2 TRP A 19 23.060 -3.306 15.000 1.00 0.00 H +ATOM 84 HB3 TRP A 19 23.734 -2.485 16.561 1.00 0.00 H +ATOM 85 CG TRP A 19 21.803 -2.993 16.678 1.00 0.00 C +ATOM 86 CD1 TRP A 19 20.917 -3.950 16.210 1.00 0.00 C +ATOM 87 HD1 TRP A 19 21.162 -4.946 15.606 1.00 0.00 H +ATOM 88 CD2 TRP A 19 21.448 -2.745 18.041 1.00 0.00 C +ATOM 89 NE1 TRP A 19 20.060 -4.304 17.222 1.00 0.00 N +ATOM 90 HE1 TRP A 19 19.166 -5.082 17.130 1.00 0.00 H +ATOM 91 CE2 TRP A 19 20.357 -3.624 18.372 1.00 0.00 C +ATOM 92 CE3 TRP A 19 21.879 -1.892 19.048 1.00 0.00 C +ATOM 93 HE3 TRP A 19 23.012 -1.653 19.280 1.00 0.00 H +ATOM 94 CZ2 TRP A 19 19.784 -3.690 19.612 1.00 0.00 C +ATOM 95 HZ2 TRP A 19 18.893 -4.428 19.882 1.00 0.00 H +ATOM 96 CZ3 TRP A 19 21.292 -1.950 20.288 1.00 0.00 C +ATOM 97 HZ3 TRP A 19 21.593 -1.341 21.264 1.00 0.00 H +ATOM 98 CH2 TRP A 19 20.230 -2.805 20.601 1.00 0.00 C +ATOM 99 HH2 TRP A 19 19.699 -2.847 21.664 1.00 0.00 H +ATOM 100 N ILE A 20 22.930 0.594 16.823 1.00 0.00 N +ATOM 101 H ILE A 20 24.076 0.541 16.550 1.00 0.00 H +ATOM 102 CA ILE A 20 22.628 1.633 17.766 1.00 0.00 C +ATOM 103 HA ILE A 20 21.789 1.290 18.542 1.00 0.00 H +ATOM 104 C ILE A 20 21.917 2.819 17.080 1.00 0.00 C +ATOM 105 O ILE A 20 20.942 3.365 17.655 1.00 0.00 O +ATOM 106 CB ILE A 20 23.902 2.192 18.499 1.00 0.00 C +ATOM 107 HB ILE A 20 24.715 2.724 17.819 1.00 0.00 H +ATOM 108 CG1 ILE A 20 24.481 0.986 19.363 1.00 0.00 C +ATOM 109 HG12 ILE A 20 23.788 1.030 20.353 1.00 0.00 H +ATOM 110 HG13 ILE A 20 24.628 -0.201 19.461 1.00 0.00 H +ATOM 111 CG2 ILE A 20 23.599 3.421 19.390 1.00 0.00 C +ATOM 112 HG21 ILE A 20 22.661 3.366 20.137 1.00 0.00 H +ATOM 113 HG22 ILE A 20 23.360 4.447 18.810 1.00 0.00 H +ATOM 114 HG23 ILE A 20 24.460 3.891 20.098 1.00 0.00 H +ATOM 115 CD1 ILE A 20 26.033 1.304 19.637 1.00 0.00 C +ATOM 116 HD11 ILE A 20 26.619 2.239 19.171 1.00 0.00 H +ATOM 117 HD12 ILE A 20 26.965 0.585 19.850 1.00 0.00 H +ATOM 118 HD13 ILE A 20 25.915 1.670 20.777 1.00 0.00 H +ATOM 119 N LYS A 21 22.464 3.177 15.957 1.00 0.00 N +ATOM 120 H LYS A 21 23.548 2.990 15.537 1.00 0.00 H +ATOM 121 CA LYS A 21 21.888 4.236 15.157 1.00 0.00 C +ATOM 122 HA LYS A 21 21.684 5.156 15.887 1.00 0.00 H +ATOM 123 C LYS A 21 20.436 3.910 14.752 1.00 0.00 C +ATOM 124 O LYS A 21 19.685 4.899 14.971 1.00 0.00 O +ATOM 125 CB LYS A 21 22.699 4.646 13.935 1.00 0.00 C +ATOM 126 HB2 LYS A 21 21.993 5.432 13.366 1.00 0.00 H +ATOM 127 HB3 LYS A 21 22.859 3.879 13.036 1.00 0.00 H +ATOM 128 CG LYS A 21 23.944 5.416 14.471 1.00 0.00 C +ATOM 129 HG2 LYS A 21 23.539 6.515 14.726 1.00 0.00 H +ATOM 130 HG3 LYS A 21 24.475 5.169 15.505 1.00 0.00 H +ATOM 131 CD LYS A 21 24.919 5.669 13.300 1.00 0.00 C +ATOM 132 HD2 LYS A 21 24.419 6.421 12.513 1.00 0.00 H +ATOM 133 HD3 LYS A 21 25.267 4.750 12.623 1.00 0.00 H +ATOM 134 CE LYS A 21 26.173 6.287 13.908 1.00 0.00 C +ATOM 135 HE2 LYS A 21 25.834 7.406 14.184 1.00 0.00 H +ATOM 136 HE3 LYS A 21 26.807 6.035 14.888 1.00 0.00 H +ATOM 137 NZ LYS A 21 27.199 6.564 12.863 1.00 0.00 N +ATOM 138 HZ1 LYS A 21 26.833 7.125 11.866 1.00 0.00 H +ATOM 139 HZ2 LYS A 21 27.890 5.710 12.384 1.00 0.00 H +ATOM 140 HZ3 LYS A 21 28.009 7.353 13.267 1.00 0.00 H +ATOM 141 N ARG A 22 20.075 2.728 14.351 1.00 0.00 N +ATOM 142 H ARG A 22 20.875 1.866 14.278 1.00 0.00 H +ATOM 143 CA ARG A 22 18.740 2.273 14.020 1.00 0.00 C +ATOM 144 HA ARG A 22 18.281 3.145 13.343 1.00 0.00 H +ATOM 145 C ARG A 22 17.807 2.365 15.177 1.00 0.00 C +ATOM 146 O ARG A 22 16.648 2.899 15.096 1.00 0.00 O +ATOM 147 CB ARG A 22 18.733 0.860 13.418 1.00 0.00 C +ATOM 148 HB2 ARG A 22 18.954 -0.058 14.146 1.00 0.00 H +ATOM 149 HB3 ARG A 22 17.556 0.698 13.252 1.00 0.00 H +ATOM 150 CG ARG A 22 19.309 0.956 12.004 1.00 0.00 C +ATOM 151 HG2 ARG A 22 18.649 1.739 11.375 1.00 0.00 H +ATOM 152 HG3 ARG A 22 20.397 1.373 11.744 1.00 0.00 H +ATOM 153 CD ARG A 22 19.117 -0.300 11.254 1.00 0.00 C +ATOM 154 HD2 ARG A 22 19.518 -0.186 10.130 1.00 0.00 H +ATOM 155 HD3 ARG A 22 17.968 -0.467 10.943 1.00 0.00 H +ATOM 156 NE ARG A 22 19.382 -1.562 11.991 1.00 0.00 N +ATOM 157 HE ARG A 22 18.475 -2.310 12.190 1.00 0.00 H +ATOM 158 CZ ARG A 22 20.624 -2.104 11.889 1.00 0.00 C +ATOM 159 NH1 ARG A 22 21.664 -1.554 11.252 1.00 0.00 N +ATOM 160 HH11 ARG A 22 21.542 -1.383 10.077 1.00 0.00 H +ATOM 161 HH12 ARG A 22 22.689 -2.158 11.323 1.00 0.00 H +ATOM 162 NH2 ARG A 22 20.870 -3.271 12.498 1.00 0.00 N +ATOM 163 HH21 ARG A 22 20.997 -4.155 11.703 1.00 0.00 H +ATOM 164 HH22 ARG A 22 20.378 -3.797 13.442 1.00 0.00 H +ATOM 165 OXT ARG A 22 18.610 1.777 15.932 1.00 0.00 O +TER 166 ARG A 22 +END diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2/2mlt_frag2_A.gro b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2/2mlt_frag2_A.gro new file mode 100644 index 00000000..83dbe89a --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2/2mlt_frag2_A.gro @@ -0,0 +1,167 @@ + Structure-Based gro file + 165 + 14 PRO N 1 3.169 -0.198 1.411 + 14 PRO H2 2 3.128 -0.295 1.466 + 14 PRO H3 3 3.18 -0.123 1.503 + 14 PRO CA 4 3.103 -0.128 1.303 + 14 PRO HA 5 3.109 -0.009 1.307 + 14 PRO C 6 2.952 -0.167 1.286 + 14 PRO O 7 2.866 -0.08 1.274 + 14 PRO CB 8 3.184 -0.161 1.182 + 14 PRO HB2 9 3.136 -0.228 1.095 + 14 PRO HB3 10 3.21 -0.065 1.115 + 14 PRO CG 11 3.312 -0.22 1.23 + 14 PRO HG2 12 3.335 -0.324 1.175 + 14 PRO HG3 13 3.408 -0.157 1.197 + 14 PRO CD 14 3.31 -0.236 1.377 + 14 PRO HD2 15 3.394 -0.171 1.431 + 14 PRO HD3 16 3.346 -0.346 1.409 + 15 ALA N 17 2.921 -0.295 1.287 + 15 ALA H 18 3.0 -0.379 1.261 + 15 ALA CA 19 2.782 -0.342 1.272 + 15 ALA HA 20 2.746 -0.294 1.169 + 15 ALA C 21 2.702 -0.302 1.395 + 15 ALA O 22 2.587 -0.255 1.377 + 15 ALA CB 23 2.774 -0.491 1.25 + 15 ALA HB1 24 2.696 -0.512 1.161 + 15 ALA HB2 25 2.73 -0.56 1.337 + 15 ALA HB3 26 2.866 -0.556 1.21 + 16 LEU N 27 2.757 -0.312 1.513 + 16 LEU H 28 2.831 -0.404 1.523 + 16 LEU CA 29 2.696 -0.265 1.635 + 16 LEU HA 30 2.604 -0.341 1.637 + 16 LEU C 31 2.661 -0.117 1.634 + 16 LEU O 32 2.56 -0.073 1.693 + 16 LEU CB 33 2.781 -0.303 1.754 + 16 LEU HB2 34 2.894 -0.267 1.736 + 16 LEU HB3 35 2.793 -0.422 1.761 + 16 LEU CG 36 2.738 -0.255 1.892 + 16 LEU HG 37 2.751 -0.137 1.902 + 16 LEU CD1 38 2.603 -0.323 1.926 + 16 LEU HD11 39 2.499 -0.284 1.883 + 16 LEU HD12 40 2.586 -0.316 2.044 + 16 LEU HD13 41 2.596 -0.442 1.911 + 16 LEU CD2 42 2.844 -0.297 1.993 + 16 LEU HD21 43 2.832 -0.404 2.045 + 16 LEU HD22 44 2.961 -0.304 1.966 + 16 LEU HD23 45 2.85 -0.224 2.088 + 17 ILE N 46 2.751 -0.037 1.579 + 17 ILE H 47 2.863 -0.076 1.57 + 17 ILE CA 48 2.734 0.106 1.562 + 17 ILE HA 49 2.713 0.146 1.672 + 17 ILE C 50 2.608 0.139 1.476 + 17 ILE O 51 2.538 0.224 1.528 + 17 ILE CB 52 2.858 0.185 1.513 + 17 ILE HB 53 2.923 0.145 1.422 + 17 ILE CG1 54 2.959 0.186 1.635 + 17 ILE HG12 55 2.916 0.246 1.73 + 17 ILE HG13 56 3.004 0.083 1.679 + 17 ILE CG2 57 2.827 0.329 1.469 + 17 ILE HG21 58 2.804 0.327 1.352 + 17 ILE HG22 59 2.914 0.412 1.466 + 17 ILE HG23 60 2.751 0.379 1.547 + 17 ILE CD1 61 3.086 0.27 1.616 + 17 ILE HD11 62 3.146 0.273 1.72 + 17 ILE HD12 63 3.166 0.22 1.542 + 17 ILE HD13 64 3.097 0.386 1.588 + 18 SER N 65 2.593 0.076 1.366 + 18 SER H 66 2.691 0.08 1.299 + 18 SER CA 67 2.483 0.083 1.274 + 18 SER HA 68 2.469 0.194 1.233 + 18 SER C 69 2.35 0.041 1.344 + 18 SER O 70 2.256 0.116 1.335 + 18 SER CB 71 2.508 0.004 1.149 + 18 SER HB2 72 2.529 -0.113 1.132 + 18 SER HB3 73 2.595 0.048 1.08 + 18 SER OG 74 2.39 0.005 1.067 + 18 SER HG 75 2.401 0.088 0.983 + 19 TRP N 76 2.351 -0.066 1.416 + 19 TRP H 77 2.404 -0.159 1.364 + 19 TRP CA 78 2.249 -0.109 1.508 + 19 TRP HA 79 2.148 -0.137 1.452 + 19 TRP C 80 2.208 0.0 1.601 + 19 TRP O 81 2.082 0.024 1.616 + 19 TRP CB 82 2.285 -0.241 1.577 + 19 TRP HB2 83 2.306 -0.331 1.5 + 19 TRP HB3 84 2.373 -0.248 1.656 + 19 TRP CG 85 2.18 -0.299 1.668 + 19 TRP CD1 86 2.092 -0.395 1.621 + 19 TRP HD1 87 2.116 -0.495 1.561 + 19 TRP CD2 88 2.145 -0.274 1.804 + 19 TRP NE1 89 2.006 -0.43 1.722 + 19 TRP HE1 90 1.917 -0.508 1.713 + 19 TRP CE2 91 2.036 -0.362 1.837 + 19 TRP CE3 92 2.188 -0.189 1.905 + 19 TRP HE3 93 2.301 -0.165 1.928 + 19 TRP CZ2 94 1.978 -0.369 1.961 + 19 TRP HZ2 95 1.889 -0.443 1.988 + 19 TRP CZ3 96 2.129 -0.195 2.029 + 19 TRP HZ3 97 2.159 -0.134 2.126 + 19 TRP CH2 98 2.023 -0.281 2.06 + 19 TRP HH2 99 1.97 -0.285 2.166 + 20 ILE N 100 2.293 0.059 1.682 + 20 ILE H 101 2.408 0.054 1.655 + 20 ILE CA 102 2.263 0.163 1.777 + 20 ILE HA 103 2.179 0.129 1.854 + 20 ILE C 104 2.192 0.282 1.708 + 20 ILE O 105 2.094 0.337 1.766 + 20 ILE CB 106 2.39 0.219 1.85 + 20 ILE HB 107 2.472 0.272 1.782 + 20 ILE CG1 108 2.448 0.099 1.936 + 20 ILE HG12 109 2.379 0.103 2.035 + 20 ILE HG13 110 2.463 -0.02 1.946 + 20 ILE CG2 111 2.36 0.342 1.939 + 20 ILE HG21 112 2.266 0.337 2.014 + 20 ILE HG22 113 2.336 0.445 1.881 + 20 ILE HG23 114 2.446 0.389 2.01 + 20 ILE CD1 115 2.603 0.13 1.964 + 20 ILE HD11 116 2.662 0.224 1.917 + 20 ILE HD12 117 2.697 0.058 1.985 + 20 ILE HD13 118 2.592 0.167 2.078 + 21 LYS N 119 2.246 0.318 1.596 + 21 LYS H 120 2.355 0.299 1.554 + 21 LYS CA 121 2.189 0.424 1.516 + 21 LYS HA 122 2.168 0.516 1.589 + 21 LYS C 123 2.044 0.391 1.475 + 21 LYS O 124 1.968 0.49 1.497 + 21 LYS CB 125 2.27 0.465 1.394 + 21 LYS HB2 126 2.199 0.543 1.337 + 21 LYS HB3 127 2.286 0.388 1.304 + 21 LYS CG 128 2.394 0.542 1.447 + 21 LYS HG2 129 2.354 0.651 1.473 + 21 LYS HG3 130 2.448 0.517 1.551 + 21 LYS CD 131 2.492 0.567 1.33 + 21 LYS HD2 132 2.442 0.642 1.251 + 21 LYS HD3 133 2.527 0.475 1.262 + 21 LYS CE 134 2.617 0.629 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b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2/burial_gamma.dat new file mode 100644 index 00000000..cca412ce --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2/burial_gamma.dat @@ -0,0 +1,20 @@ +0.839477E+00 0.877743E+00 0.574228E+00 +0.937289E+00 0.832808E+00 0.128733E+00 +0.957784E+00 0.787425E+00 0.247626E+00 +0.975863E+00 0.752419E+00 0.203863E+00 +0.674794E+00 0.942934E+00 0.657798E+00 +0.956183E+00 0.791729E+00 0.237100E+00 +0.966898E+00 0.777267E+00 0.159117E+00 +0.937239E+00 0.809261E+00 0.342555E+00 +0.921287E+00 0.852423E+00 0.127282E+00 +0.777337E+00 0.924703E+00 0.545743E+00 +0.784304E+00 0.936113E+00 0.459918E+00 +0.983039E+00 0.747093E+00 0.137667E-02 +0.815739E+00 0.915572E+00 0.458737E+00 +0.809499E+00 0.937816E+00 0.333302E+00 +0.965914E+00 0.762021E+00 0.252445E+00 +0.943312E+00 0.794870E+00 0.380930E+00 +0.924437E+00 0.819165E+00 0.402452E+00 +0.853591E+00 0.905143E+00 0.341284E+00 +0.834249E+00 0.919286E+00 0.344424E+00 +0.766891E+00 0.929200E+00 0.548487E+00 diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2/charge.txt b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2/charge.txt new file mode 100644 index 00000000..29857a3c --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2/charge.txt @@ -0,0 +1,9 @@ +0 0.0 +1 0.0 +2 0.0 +3 0.0 +4 0.0 +5 0.0 +6 0.0 +7 1.0 +8 1.0 diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2/cleaned_pdbs/2mlt_frag2.pdb b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2/cleaned_pdbs/2mlt_frag2.pdb new file mode 100644 index 00000000..b1f527a9 --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2/cleaned_pdbs/2mlt_frag2.pdb @@ -0,0 +1,169 @@ +REMARK 1 CREATED WITH OPENMM 8.1.1, 2025-12-23 +CRYST1 60.832 38.293 42.211 90.00 90.00 90.00 P 1 1 +ATOM 1 N PRO A 14 31.689 -1.979 14.106 1.00 0.00 N +ATOM 2 H2 PRO A 14 31.276 -2.955 14.661 1.00 0.00 H +ATOM 3 H3 PRO A 14 31.802 -1.230 15.035 1.00 0.00 H +ATOM 4 CA PRO A 14 31.026 -1.278 13.030 1.00 0.00 C +ATOM 5 HA PRO A 14 31.087 -0.087 13.067 1.00 0.00 H +ATOM 6 C PRO A 14 29.521 -1.670 12.857 1.00 0.00 C +ATOM 7 O PRO A 14 28.657 -0.801 12.744 1.00 0.00 O +ATOM 8 CB PRO A 14 31.845 -1.614 11.816 1.00 0.00 C +ATOM 9 HB2 PRO A 14 31.360 -2.281 10.948 1.00 0.00 H +ATOM 10 HB3 PRO A 14 32.105 -0.652 11.150 1.00 0.00 H +ATOM 11 CG PRO A 14 33.118 -2.205 12.303 1.00 0.00 C +ATOM 12 HG2 PRO A 14 33.354 -3.243 11.750 1.00 0.00 H +ATOM 13 HG3 PRO A 14 34.080 -1.569 11.972 1.00 0.00 H +ATOM 14 CD PRO A 14 33.098 -2.363 13.769 1.00 0.00 C +ATOM 15 HD2 PRO A 14 33.941 -1.705 14.312 1.00 0.00 H +ATOM 16 HD3 PRO A 14 33.456 -3.462 14.092 1.00 0.00 H +ATOM 17 N ALA A 15 29.207 -2.952 12.868 1.00 0.00 N +ATOM 18 H ALA A 15 30.005 -3.794 12.606 1.00 0.00 H +ATOM 19 CA ALA A 15 27.822 -3.418 12.724 1.00 0.00 C +ATOM 20 HA ALA A 15 27.464 -2.944 11.690 1.00 0.00 H +ATOM 21 C ALA A 15 27.023 -3.016 13.951 1.00 0.00 C +ATOM 22 O ALA A 15 25.872 -2.551 13.769 1.00 0.00 O +ATOM 23 CB ALA A 15 27.741 -4.906 12.502 1.00 0.00 C +ATOM 24 HB1 ALA A 15 26.960 -5.122 11.612 1.00 0.00 H +ATOM 25 HB2 ALA A 15 27.299 -5.602 13.372 1.00 0.00 H +ATOM 26 HB3 ALA A 15 28.660 -5.560 12.095 1.00 0.00 H +ATOM 27 N LEU A 16 27.570 -3.117 15.127 1.00 0.00 N +ATOM 28 H LEU A 16 28.311 -4.043 15.235 1.00 0.00 H +ATOM 29 CA LEU A 16 26.958 -2.649 16.351 1.00 0.00 C +ATOM 30 HA LEU A 16 26.042 -3.413 16.370 1.00 0.00 H +ATOM 31 C LEU A 16 26.614 -1.169 16.344 1.00 0.00 C +ATOM 32 O LEU A 16 25.599 -0.734 16.933 1.00 0.00 O +ATOM 33 CB LEU A 16 27.811 -3.027 17.542 1.00 0.00 C +ATOM 34 HB2 LEU A 16 28.937 -2.668 17.356 1.00 0.00 H +ATOM 35 HB3 LEU A 16 27.935 -4.219 17.610 1.00 0.00 H +ATOM 36 CG LEU A 16 27.384 -2.550 18.921 1.00 0.00 C +ATOM 37 HG LEU A 16 27.514 -1.374 19.018 1.00 0.00 H +ATOM 38 CD1 LEU A 16 26.031 -3.234 19.257 1.00 0.00 C +ATOM 39 HD11 LEU A 16 24.991 -2.840 18.834 1.00 0.00 H +ATOM 40 HD12 LEU A 16 25.864 -3.158 20.443 1.00 0.00 H +ATOM 41 HD13 LEU A 16 25.963 -4.423 19.106 1.00 0.00 H +ATOM 42 CD2 LEU A 16 28.445 -2.970 19.933 1.00 0.00 C +ATOM 43 HD21 LEU A 16 28.316 -4.043 20.454 1.00 0.00 H +ATOM 44 HD22 LEU A 16 29.611 -3.035 19.656 1.00 0.00 H +ATOM 45 HD23 LEU A 16 28.497 -2.237 20.881 1.00 0.00 H +ATOM 46 N ILE A 17 27.514 -0.365 15.791 1.00 0.00 N +ATOM 47 H ILE A 17 28.628 -0.758 15.698 1.00 0.00 H +ATOM 48 CA ILE A 17 27.343 1.056 15.618 1.00 0.00 C +ATOM 49 HA ILE A 17 27.131 1.458 16.719 1.00 0.00 H +ATOM 50 C ILE A 17 26.081 1.392 14.758 1.00 0.00 C +ATOM 51 O ILE A 17 25.380 2.240 15.282 1.00 0.00 O +ATOM 52 CB ILE A 17 28.579 1.847 15.132 1.00 0.00 C +ATOM 53 HB ILE A 17 29.228 1.447 14.218 1.00 0.00 H +ATOM 54 CG1 ILE A 17 29.586 1.858 16.352 1.00 0.00 C +ATOM 55 HG12 ILE A 17 29.162 2.458 17.298 1.00 0.00 H +ATOM 56 HG13 ILE A 17 30.039 0.835 16.791 1.00 0.00 H +ATOM 57 CG2 ILE A 17 28.268 3.288 14.691 1.00 0.00 C +ATOM 58 HG21 ILE A 17 28.042 3.268 13.517 1.00 0.00 H +ATOM 59 HG22 ILE A 17 29.137 4.118 14.665 1.00 0.00 H +ATOM 60 HG23 ILE A 17 27.512 3.793 15.466 1.00 0.00 H +ATOM 61 CD1 ILE A 17 30.856 2.696 16.161 1.00 0.00 C +ATOM 62 HD11 ILE A 17 31.458 2.727 17.204 1.00 0.00 H +ATOM 63 HD12 ILE A 17 31.660 2.198 15.423 1.00 0.00 H +ATOM 64 HD13 ILE A 17 30.974 3.856 15.882 1.00 0.00 H +ATOM 65 N SER A 18 25.930 0.759 13.657 1.00 0.00 N +ATOM 66 H SER A 18 26.912 0.800 12.987 1.00 0.00 H +ATOM 67 CA SER A 18 24.825 0.827 12.744 1.00 0.00 C +ATOM 68 HA SER A 18 24.692 1.936 12.326 1.00 0.00 H +ATOM 69 C SER A 18 23.499 0.405 13.438 1.00 0.00 C +ATOM 70 O SER A 18 22.557 1.165 13.352 1.00 0.00 O +ATOM 71 CB SER A 18 25.076 0.039 11.491 1.00 0.00 C +ATOM 72 HB2 SER A 18 25.292 -1.128 11.323 1.00 0.00 H +ATOM 73 HB3 SER A 18 25.948 0.476 10.797 1.00 0.00 H +ATOM 74 OG SER A 18 23.902 0.046 10.670 1.00 0.00 O +ATOM 75 HG SER A 18 24.014 0.879 9.826 1.00 0.00 H +ATOM 76 N TRP A 19 23.512 -0.661 14.161 1.00 0.00 N +ATOM 77 H TRP A 19 24.036 -1.593 13.643 1.00 0.00 H +ATOM 78 CA TRP A 19 22.492 -1.085 15.081 1.00 0.00 C +ATOM 79 HA TRP A 19 21.482 -1.368 14.518 1.00 0.00 H +ATOM 80 C TRP A 19 22.083 0.004 16.012 1.00 0.00 C +ATOM 81 O TRP A 19 20.820 0.244 16.160 1.00 0.00 O +ATOM 82 CB TRP A 19 22.854 -2.410 15.767 1.00 0.00 C +ATOM 83 HB2 TRP A 19 23.060 -3.306 15.000 1.00 0.00 H +ATOM 84 HB3 TRP A 19 23.734 -2.485 16.561 1.00 0.00 H +ATOM 85 CG TRP A 19 21.803 -2.993 16.678 1.00 0.00 C +ATOM 86 CD1 TRP A 19 20.917 -3.950 16.210 1.00 0.00 C +ATOM 87 HD1 TRP A 19 21.162 -4.946 15.606 1.00 0.00 H +ATOM 88 CD2 TRP A 19 21.448 -2.745 18.041 1.00 0.00 C +ATOM 89 NE1 TRP A 19 20.060 -4.304 17.222 1.00 0.00 N +ATOM 90 HE1 TRP A 19 19.166 -5.082 17.130 1.00 0.00 H +ATOM 91 CE2 TRP A 19 20.357 -3.624 18.372 1.00 0.00 C +ATOM 92 CE3 TRP A 19 21.879 -1.892 19.048 1.00 0.00 C +ATOM 93 HE3 TRP A 19 23.012 -1.653 19.280 1.00 0.00 H +ATOM 94 CZ2 TRP A 19 19.784 -3.690 19.612 1.00 0.00 C +ATOM 95 HZ2 TRP A 19 18.893 -4.428 19.882 1.00 0.00 H +ATOM 96 CZ3 TRP A 19 21.292 -1.950 20.288 1.00 0.00 C +ATOM 97 HZ3 TRP A 19 21.593 -1.341 21.264 1.00 0.00 H +ATOM 98 CH2 TRP A 19 20.230 -2.805 20.601 1.00 0.00 C +ATOM 99 HH2 TRP A 19 19.699 -2.847 21.664 1.00 0.00 H +ATOM 100 N ILE A 20 22.930 0.594 16.823 1.00 0.00 N +ATOM 101 H ILE A 20 24.076 0.541 16.550 1.00 0.00 H +ATOM 102 CA ILE A 20 22.628 1.633 17.766 1.00 0.00 C +ATOM 103 HA ILE A 20 21.789 1.290 18.542 1.00 0.00 H +ATOM 104 C ILE A 20 21.917 2.819 17.080 1.00 0.00 C +ATOM 105 O ILE A 20 20.942 3.365 17.655 1.00 0.00 O +ATOM 106 CB ILE A 20 23.902 2.192 18.499 1.00 0.00 C +ATOM 107 HB ILE A 20 24.715 2.724 17.819 1.00 0.00 H +ATOM 108 CG1 ILE A 20 24.481 0.986 19.363 1.00 0.00 C +ATOM 109 HG12 ILE A 20 23.788 1.030 20.353 1.00 0.00 H +ATOM 110 HG13 ILE A 20 24.628 -0.201 19.461 1.00 0.00 H +ATOM 111 CG2 ILE A 20 23.599 3.421 19.390 1.00 0.00 C +ATOM 112 HG21 ILE A 20 22.661 3.366 20.137 1.00 0.00 H +ATOM 113 HG22 ILE A 20 23.360 4.447 18.810 1.00 0.00 H +ATOM 114 HG23 ILE A 20 24.460 3.891 20.098 1.00 0.00 H +ATOM 115 CD1 ILE A 20 26.033 1.304 19.637 1.00 0.00 C +ATOM 116 HD11 ILE A 20 26.619 2.239 19.171 1.00 0.00 H +ATOM 117 HD12 ILE A 20 26.965 0.585 19.850 1.00 0.00 H +ATOM 118 HD13 ILE A 20 25.915 1.670 20.777 1.00 0.00 H +ATOM 119 N LYS A 21 22.464 3.177 15.957 1.00 0.00 N +ATOM 120 H LYS A 21 23.548 2.990 15.537 1.00 0.00 H +ATOM 121 CA LYS A 21 21.888 4.236 15.157 1.00 0.00 C +ATOM 122 HA LYS A 21 21.684 5.156 15.887 1.00 0.00 H +ATOM 123 C LYS A 21 20.436 3.910 14.752 1.00 0.00 C +ATOM 124 O LYS A 21 19.685 4.899 14.971 1.00 0.00 O +ATOM 125 CB LYS A 21 22.699 4.646 13.935 1.00 0.00 C +ATOM 126 HB2 LYS A 21 21.993 5.432 13.366 1.00 0.00 H +ATOM 127 HB3 LYS A 21 22.859 3.879 13.036 1.00 0.00 H +ATOM 128 CG LYS A 21 23.944 5.416 14.471 1.00 0.00 C +ATOM 129 HG2 LYS A 21 23.539 6.515 14.726 1.00 0.00 H +ATOM 130 HG3 LYS A 21 24.475 5.169 15.505 1.00 0.00 H +ATOM 131 CD LYS A 21 24.919 5.669 13.300 1.00 0.00 C +ATOM 132 HD2 LYS A 21 24.419 6.421 12.513 1.00 0.00 H +ATOM 133 HD3 LYS A 21 25.267 4.750 12.623 1.00 0.00 H +ATOM 134 CE LYS A 21 26.173 6.287 13.908 1.00 0.00 C +ATOM 135 HE2 LYS A 21 25.834 7.406 14.184 1.00 0.00 H +ATOM 136 HE3 LYS A 21 26.807 6.035 14.888 1.00 0.00 H +ATOM 137 NZ LYS A 21 27.199 6.564 12.863 1.00 0.00 N +ATOM 138 HZ1 LYS A 21 26.833 7.125 11.866 1.00 0.00 H +ATOM 139 HZ2 LYS A 21 27.890 5.710 12.384 1.00 0.00 H +ATOM 140 HZ3 LYS A 21 28.009 7.353 13.267 1.00 0.00 H +ATOM 141 N ARG A 22 20.075 2.728 14.351 1.00 0.00 N +ATOM 142 H ARG A 22 20.875 1.866 14.278 1.00 0.00 H +ATOM 143 CA ARG A 22 18.740 2.273 14.020 1.00 0.00 C +ATOM 144 HA ARG A 22 18.281 3.145 13.343 1.00 0.00 H +ATOM 145 C ARG A 22 17.807 2.365 15.177 1.00 0.00 C +ATOM 146 O ARG A 22 16.648 2.899 15.096 1.00 0.00 O +ATOM 147 CB ARG A 22 18.733 0.860 13.418 1.00 0.00 C +ATOM 148 HB2 ARG A 22 18.954 -0.058 14.146 1.00 0.00 H +ATOM 149 HB3 ARG A 22 17.556 0.698 13.252 1.00 0.00 H +ATOM 150 CG ARG A 22 19.309 0.956 12.004 1.00 0.00 C +ATOM 151 HG2 ARG A 22 18.649 1.739 11.375 1.00 0.00 H +ATOM 152 HG3 ARG A 22 20.397 1.373 11.744 1.00 0.00 H +ATOM 153 CD ARG A 22 19.117 -0.300 11.254 1.00 0.00 C +ATOM 154 HD2 ARG A 22 19.518 -0.186 10.130 1.00 0.00 H +ATOM 155 HD3 ARG A 22 17.968 -0.467 10.943 1.00 0.00 H +ATOM 156 NE ARG A 22 19.382 -1.562 11.991 1.00 0.00 N +ATOM 157 HE ARG A 22 18.475 -2.310 12.190 1.00 0.00 H +ATOM 158 CZ ARG A 22 20.624 -2.104 11.889 1.00 0.00 C +ATOM 159 NH1 ARG A 22 21.664 -1.554 11.252 1.00 0.00 N +ATOM 160 HH11 ARG A 22 21.542 -1.383 10.077 1.00 0.00 H +ATOM 161 HH12 ARG A 22 22.689 -2.158 11.323 1.00 0.00 H +ATOM 162 NH2 ARG A 22 20.870 -3.271 12.498 1.00 0.00 N +ATOM 163 HH21 ARG A 22 20.997 -4.155 11.703 1.00 0.00 H +ATOM 164 HH22 ARG A 22 20.378 -3.797 13.442 1.00 0.00 H +ATOM 165 OXT ARG A 22 18.610 1.777 15.932 1.00 0.00 O +TER 166 ARG A 22 +END diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2/crystal_structure-cleaned.pdb b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2/crystal_structure-cleaned.pdb new file mode 100644 index 00000000..b1f527a9 --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2/crystal_structure-cleaned.pdb @@ -0,0 +1,169 @@ +REMARK 1 CREATED WITH OPENMM 8.1.1, 2025-12-23 +CRYST1 60.832 38.293 42.211 90.00 90.00 90.00 P 1 1 +ATOM 1 N PRO A 14 31.689 -1.979 14.106 1.00 0.00 N +ATOM 2 H2 PRO A 14 31.276 -2.955 14.661 1.00 0.00 H +ATOM 3 H3 PRO A 14 31.802 -1.230 15.035 1.00 0.00 H +ATOM 4 CA PRO A 14 31.026 -1.278 13.030 1.00 0.00 C +ATOM 5 HA PRO A 14 31.087 -0.087 13.067 1.00 0.00 H +ATOM 6 C PRO A 14 29.521 -1.670 12.857 1.00 0.00 C +ATOM 7 O PRO A 14 28.657 -0.801 12.744 1.00 0.00 O +ATOM 8 CB PRO A 14 31.845 -1.614 11.816 1.00 0.00 C +ATOM 9 HB2 PRO A 14 31.360 -2.281 10.948 1.00 0.00 H +ATOM 10 HB3 PRO A 14 32.105 -0.652 11.150 1.00 0.00 H +ATOM 11 CG PRO A 14 33.118 -2.205 12.303 1.00 0.00 C +ATOM 12 HG2 PRO A 14 33.354 -3.243 11.750 1.00 0.00 H +ATOM 13 HG3 PRO A 14 34.080 -1.569 11.972 1.00 0.00 H +ATOM 14 CD PRO A 14 33.098 -2.363 13.769 1.00 0.00 C +ATOM 15 HD2 PRO A 14 33.941 -1.705 14.312 1.00 0.00 H +ATOM 16 HD3 PRO A 14 33.456 -3.462 14.092 1.00 0.00 H +ATOM 17 N ALA A 15 29.207 -2.952 12.868 1.00 0.00 N +ATOM 18 H ALA A 15 30.005 -3.794 12.606 1.00 0.00 H +ATOM 19 CA ALA A 15 27.822 -3.418 12.724 1.00 0.00 C +ATOM 20 HA ALA A 15 27.464 -2.944 11.690 1.00 0.00 H +ATOM 21 C ALA A 15 27.023 -3.016 13.951 1.00 0.00 C +ATOM 22 O ALA A 15 25.872 -2.551 13.769 1.00 0.00 O +ATOM 23 CB ALA A 15 27.741 -4.906 12.502 1.00 0.00 C +ATOM 24 HB1 ALA A 15 26.960 -5.122 11.612 1.00 0.00 H +ATOM 25 HB2 ALA A 15 27.299 -5.602 13.372 1.00 0.00 H +ATOM 26 HB3 ALA A 15 28.660 -5.560 12.095 1.00 0.00 H +ATOM 27 N LEU A 16 27.570 -3.117 15.127 1.00 0.00 N +ATOM 28 H LEU A 16 28.311 -4.043 15.235 1.00 0.00 H +ATOM 29 CA LEU A 16 26.958 -2.649 16.351 1.00 0.00 C +ATOM 30 HA LEU A 16 26.042 -3.413 16.370 1.00 0.00 H +ATOM 31 C LEU A 16 26.614 -1.169 16.344 1.00 0.00 C +ATOM 32 O LEU A 16 25.599 -0.734 16.933 1.00 0.00 O +ATOM 33 CB LEU A 16 27.811 -3.027 17.542 1.00 0.00 C +ATOM 34 HB2 LEU A 16 28.937 -2.668 17.356 1.00 0.00 H +ATOM 35 HB3 LEU A 16 27.935 -4.219 17.610 1.00 0.00 H +ATOM 36 CG LEU A 16 27.384 -2.550 18.921 1.00 0.00 C +ATOM 37 HG LEU A 16 27.514 -1.374 19.018 1.00 0.00 H +ATOM 38 CD1 LEU A 16 26.031 -3.234 19.257 1.00 0.00 C +ATOM 39 HD11 LEU A 16 24.991 -2.840 18.834 1.00 0.00 H +ATOM 40 HD12 LEU A 16 25.864 -3.158 20.443 1.00 0.00 H +ATOM 41 HD13 LEU A 16 25.963 -4.423 19.106 1.00 0.00 H +ATOM 42 CD2 LEU A 16 28.445 -2.970 19.933 1.00 0.00 C +ATOM 43 HD21 LEU A 16 28.316 -4.043 20.454 1.00 0.00 H +ATOM 44 HD22 LEU A 16 29.611 -3.035 19.656 1.00 0.00 H +ATOM 45 HD23 LEU A 16 28.497 -2.237 20.881 1.00 0.00 H +ATOM 46 N ILE A 17 27.514 -0.365 15.791 1.00 0.00 N +ATOM 47 H ILE A 17 28.628 -0.758 15.698 1.00 0.00 H +ATOM 48 CA ILE A 17 27.343 1.056 15.618 1.00 0.00 C +ATOM 49 HA ILE A 17 27.131 1.458 16.719 1.00 0.00 H +ATOM 50 C ILE A 17 26.081 1.392 14.758 1.00 0.00 C +ATOM 51 O ILE A 17 25.380 2.240 15.282 1.00 0.00 O +ATOM 52 CB ILE A 17 28.579 1.847 15.132 1.00 0.00 C +ATOM 53 HB ILE A 17 29.228 1.447 14.218 1.00 0.00 H +ATOM 54 CG1 ILE A 17 29.586 1.858 16.352 1.00 0.00 C +ATOM 55 HG12 ILE A 17 29.162 2.458 17.298 1.00 0.00 H +ATOM 56 HG13 ILE A 17 30.039 0.835 16.791 1.00 0.00 H +ATOM 57 CG2 ILE A 17 28.268 3.288 14.691 1.00 0.00 C +ATOM 58 HG21 ILE A 17 28.042 3.268 13.517 1.00 0.00 H +ATOM 59 HG22 ILE A 17 29.137 4.118 14.665 1.00 0.00 H +ATOM 60 HG23 ILE A 17 27.512 3.793 15.466 1.00 0.00 H +ATOM 61 CD1 ILE A 17 30.856 2.696 16.161 1.00 0.00 C +ATOM 62 HD11 ILE A 17 31.458 2.727 17.204 1.00 0.00 H +ATOM 63 HD12 ILE A 17 31.660 2.198 15.423 1.00 0.00 H +ATOM 64 HD13 ILE A 17 30.974 3.856 15.882 1.00 0.00 H +ATOM 65 N SER A 18 25.930 0.759 13.657 1.00 0.00 N +ATOM 66 H SER A 18 26.912 0.800 12.987 1.00 0.00 H +ATOM 67 CA SER A 18 24.825 0.827 12.744 1.00 0.00 C +ATOM 68 HA SER A 18 24.692 1.936 12.326 1.00 0.00 H +ATOM 69 C SER A 18 23.499 0.405 13.438 1.00 0.00 C +ATOM 70 O SER A 18 22.557 1.165 13.352 1.00 0.00 O +ATOM 71 CB SER A 18 25.076 0.039 11.491 1.00 0.00 C +ATOM 72 HB2 SER A 18 25.292 -1.128 11.323 1.00 0.00 H +ATOM 73 HB3 SER A 18 25.948 0.476 10.797 1.00 0.00 H +ATOM 74 OG SER A 18 23.902 0.046 10.670 1.00 0.00 O +ATOM 75 HG SER A 18 24.014 0.879 9.826 1.00 0.00 H +ATOM 76 N TRP A 19 23.512 -0.661 14.161 1.00 0.00 N +ATOM 77 H TRP A 19 24.036 -1.593 13.643 1.00 0.00 H +ATOM 78 CA TRP A 19 22.492 -1.085 15.081 1.00 0.00 C +ATOM 79 HA TRP A 19 21.482 -1.368 14.518 1.00 0.00 H +ATOM 80 C TRP A 19 22.083 0.004 16.012 1.00 0.00 C +ATOM 81 O TRP A 19 20.820 0.244 16.160 1.00 0.00 O +ATOM 82 CB TRP A 19 22.854 -2.410 15.767 1.00 0.00 C +ATOM 83 HB2 TRP A 19 23.060 -3.306 15.000 1.00 0.00 H +ATOM 84 HB3 TRP A 19 23.734 -2.485 16.561 1.00 0.00 H +ATOM 85 CG TRP A 19 21.803 -2.993 16.678 1.00 0.00 C +ATOM 86 CD1 TRP A 19 20.917 -3.950 16.210 1.00 0.00 C +ATOM 87 HD1 TRP A 19 21.162 -4.946 15.606 1.00 0.00 H +ATOM 88 CD2 TRP A 19 21.448 -2.745 18.041 1.00 0.00 C +ATOM 89 NE1 TRP A 19 20.060 -4.304 17.222 1.00 0.00 N +ATOM 90 HE1 TRP A 19 19.166 -5.082 17.130 1.00 0.00 H +ATOM 91 CE2 TRP A 19 20.357 -3.624 18.372 1.00 0.00 C +ATOM 92 CE3 TRP A 19 21.879 -1.892 19.048 1.00 0.00 C +ATOM 93 HE3 TRP A 19 23.012 -1.653 19.280 1.00 0.00 H +ATOM 94 CZ2 TRP A 19 19.784 -3.690 19.612 1.00 0.00 C +ATOM 95 HZ2 TRP A 19 18.893 -4.428 19.882 1.00 0.00 H +ATOM 96 CZ3 TRP A 19 21.292 -1.950 20.288 1.00 0.00 C +ATOM 97 HZ3 TRP A 19 21.593 -1.341 21.264 1.00 0.00 H +ATOM 98 CH2 TRP A 19 20.230 -2.805 20.601 1.00 0.00 C +ATOM 99 HH2 TRP A 19 19.699 -2.847 21.664 1.00 0.00 H +ATOM 100 N ILE A 20 22.930 0.594 16.823 1.00 0.00 N +ATOM 101 H ILE A 20 24.076 0.541 16.550 1.00 0.00 H +ATOM 102 CA ILE A 20 22.628 1.633 17.766 1.00 0.00 C +ATOM 103 HA ILE A 20 21.789 1.290 18.542 1.00 0.00 H +ATOM 104 C ILE A 20 21.917 2.819 17.080 1.00 0.00 C +ATOM 105 O ILE A 20 20.942 3.365 17.655 1.00 0.00 O +ATOM 106 CB ILE A 20 23.902 2.192 18.499 1.00 0.00 C +ATOM 107 HB ILE A 20 24.715 2.724 17.819 1.00 0.00 H +ATOM 108 CG1 ILE A 20 24.481 0.986 19.363 1.00 0.00 C +ATOM 109 HG12 ILE A 20 23.788 1.030 20.353 1.00 0.00 H +ATOM 110 HG13 ILE A 20 24.628 -0.201 19.461 1.00 0.00 H +ATOM 111 CG2 ILE A 20 23.599 3.421 19.390 1.00 0.00 C +ATOM 112 HG21 ILE A 20 22.661 3.366 20.137 1.00 0.00 H +ATOM 113 HG22 ILE A 20 23.360 4.447 18.810 1.00 0.00 H +ATOM 114 HG23 ILE A 20 24.460 3.891 20.098 1.00 0.00 H +ATOM 115 CD1 ILE A 20 26.033 1.304 19.637 1.00 0.00 C +ATOM 116 HD11 ILE A 20 26.619 2.239 19.171 1.00 0.00 H +ATOM 117 HD12 ILE A 20 26.965 0.585 19.850 1.00 0.00 H +ATOM 118 HD13 ILE A 20 25.915 1.670 20.777 1.00 0.00 H +ATOM 119 N LYS A 21 22.464 3.177 15.957 1.00 0.00 N +ATOM 120 H LYS A 21 23.548 2.990 15.537 1.00 0.00 H +ATOM 121 CA LYS A 21 21.888 4.236 15.157 1.00 0.00 C +ATOM 122 HA LYS A 21 21.684 5.156 15.887 1.00 0.00 H +ATOM 123 C LYS A 21 20.436 3.910 14.752 1.00 0.00 C +ATOM 124 O LYS A 21 19.685 4.899 14.971 1.00 0.00 O +ATOM 125 CB LYS A 21 22.699 4.646 13.935 1.00 0.00 C +ATOM 126 HB2 LYS A 21 21.993 5.432 13.366 1.00 0.00 H +ATOM 127 HB3 LYS A 21 22.859 3.879 13.036 1.00 0.00 H +ATOM 128 CG LYS A 21 23.944 5.416 14.471 1.00 0.00 C +ATOM 129 HG2 LYS A 21 23.539 6.515 14.726 1.00 0.00 H +ATOM 130 HG3 LYS A 21 24.475 5.169 15.505 1.00 0.00 H +ATOM 131 CD LYS A 21 24.919 5.669 13.300 1.00 0.00 C +ATOM 132 HD2 LYS A 21 24.419 6.421 12.513 1.00 0.00 H +ATOM 133 HD3 LYS A 21 25.267 4.750 12.623 1.00 0.00 H +ATOM 134 CE LYS A 21 26.173 6.287 13.908 1.00 0.00 C +ATOM 135 HE2 LYS A 21 25.834 7.406 14.184 1.00 0.00 H +ATOM 136 HE3 LYS A 21 26.807 6.035 14.888 1.00 0.00 H +ATOM 137 NZ LYS A 21 27.199 6.564 12.863 1.00 0.00 N +ATOM 138 HZ1 LYS A 21 26.833 7.125 11.866 1.00 0.00 H +ATOM 139 HZ2 LYS A 21 27.890 5.710 12.384 1.00 0.00 H +ATOM 140 HZ3 LYS A 21 28.009 7.353 13.267 1.00 0.00 H +ATOM 141 N ARG A 22 20.075 2.728 14.351 1.00 0.00 N +ATOM 142 H ARG A 22 20.875 1.866 14.278 1.00 0.00 H +ATOM 143 CA ARG A 22 18.740 2.273 14.020 1.00 0.00 C +ATOM 144 HA ARG A 22 18.281 3.145 13.343 1.00 0.00 H +ATOM 145 C ARG A 22 17.807 2.365 15.177 1.00 0.00 C +ATOM 146 O ARG A 22 16.648 2.899 15.096 1.00 0.00 O +ATOM 147 CB ARG A 22 18.733 0.860 13.418 1.00 0.00 C +ATOM 148 HB2 ARG A 22 18.954 -0.058 14.146 1.00 0.00 H +ATOM 149 HB3 ARG A 22 17.556 0.698 13.252 1.00 0.00 H +ATOM 150 CG ARG A 22 19.309 0.956 12.004 1.00 0.00 C +ATOM 151 HG2 ARG A 22 18.649 1.739 11.375 1.00 0.00 H +ATOM 152 HG3 ARG A 22 20.397 1.373 11.744 1.00 0.00 H +ATOM 153 CD ARG A 22 19.117 -0.300 11.254 1.00 0.00 C +ATOM 154 HD2 ARG A 22 19.518 -0.186 10.130 1.00 0.00 H +ATOM 155 HD3 ARG A 22 17.968 -0.467 10.943 1.00 0.00 H +ATOM 156 NE ARG A 22 19.382 -1.562 11.991 1.00 0.00 N +ATOM 157 HE ARG A 22 18.475 -2.310 12.190 1.00 0.00 H +ATOM 158 CZ ARG A 22 20.624 -2.104 11.889 1.00 0.00 C +ATOM 159 NH1 ARG A 22 21.664 -1.554 11.252 1.00 0.00 N +ATOM 160 HH11 ARG A 22 21.542 -1.383 10.077 1.00 0.00 H +ATOM 161 HH12 ARG A 22 22.689 -2.158 11.323 1.00 0.00 H +ATOM 162 NH2 ARG A 22 20.870 -3.271 12.498 1.00 0.00 N +ATOM 163 HH21 ARG A 22 20.997 -4.155 11.703 1.00 0.00 H +ATOM 164 HH22 ARG A 22 20.378 -3.797 13.442 1.00 0.00 H +ATOM 165 OXT ARG A 22 18.610 1.777 15.932 1.00 0.00 O +TER 166 ARG A 22 +END diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2/crystal_structure-openmmawsem.pdb b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2/crystal_structure-openmmawsem.pdb new file mode 100644 index 00000000..3c4c0e1a --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2/crystal_structure-openmmawsem.pdb @@ -0,0 +1,53 @@ +ATOM 1 CA IPR A 14 31.026 -1.278 13.030 1.00 0.00 C +ATOM 2 C IPR A 14 29.512 -1.628 12.866 1.00 0.00 C +ATOM 3 O IPR A 14 28.657 -0.801 12.744 1.00 0.00 O +ATOM 4 CB IPR A 14 31.845 -1.614 11.816 1.00 0.00 B +ATOM 5 N NGP A 15 29.215 -2.872 12.869 1.00 0.00 N +ATOM 6 H NGP A 15 29.906 -3.539 12.968 1.00 0.00 H +ATOM 7 CA NGP A 15 27.822 -3.418 12.724 1.00 0.00 C +ATOM 8 C NGP A 15 26.993 -2.959 13.913 1.00 0.00 C +ATOM 9 O NGP A 15 25.872 -2.551 13.769 1.00 0.00 O +ATOM 10 CB NGP A 15 27.741 -4.906 12.502 1.00 0.00 B +ATOM 11 N NGP A 16 27.579 -3.039 15.080 1.00 0.00 N +ATOM 12 H NGP A 16 28.484 -3.368 15.197 1.00 0.00 H +ATOM 13 CA NGP A 16 26.958 -2.649 16.351 1.00 0.00 C +ATOM 14 C NGP A 16 26.612 -1.163 16.366 1.00 0.00 C +ATOM 15 O NGP A 16 25.599 -0.734 16.933 1.00 0.00 O +ATOM 16 CB NGP A 16 27.811 -3.027 17.542 1.00 0.00 B +ATOM 17 N NGP A 17 27.483 -0.400 15.727 1.00 0.00 N +ATOM 18 H NGP A 17 28.301 -0.746 15.270 1.00 0.00 H +ATOM 19 CA NGP A 17 27.343 1.056 15.618 1.00 0.00 C +ATOM 20 C NGP A 17 26.120 1.382 14.834 1.00 0.00 C +ATOM 21 O NGP A 17 25.380 2.240 15.282 1.00 0.00 O +ATOM 22 CB NGP A 17 28.579 1.847 15.132 1.00 0.00 B +ATOM 23 N NGP A 18 25.939 0.674 13.660 1.00 0.00 N +ATOM 24 H NGP A 18 26.537 -0.017 13.299 1.00 0.00 H +ATOM 25 CA NGP A 18 24.825 0.827 12.744 1.00 0.00 C +ATOM 26 C NGP A 18 23.548 0.486 13.489 1.00 0.00 C +ATOM 27 O NGP A 18 22.557 1.165 13.352 1.00 0.00 O +ATOM 28 CB NGP A 18 25.076 0.039 11.491 1.00 0.00 B +ATOM 29 N NGP A 19 23.608 -0.581 14.275 1.00 0.00 N +ATOM 30 H NGP A 19 24.408 -1.128 14.386 1.00 0.00 H +ATOM 31 CA NGP A 19 22.492 -1.085 15.081 1.00 0.00 C +ATOM 32 C NGP A 19 21.987 -0.019 16.059 1.00 0.00 C +ATOM 33 O NGP A 19 20.820 0.244 16.160 1.00 0.00 O +ATOM 34 CB NGP A 19 22.854 -2.410 15.767 1.00 0.00 B +ATOM 35 N NGP A 20 22.900 0.579 16.769 1.00 0.00 N +ATOM 36 H NGP A 20 23.842 0.367 16.688 1.00 0.00 H +ATOM 37 CA NGP A 20 22.628 1.633 17.766 1.00 0.00 C +ATOM 38 C NGP A 20 21.912 2.801 17.117 1.00 0.00 C +ATOM 39 O NGP A 20 20.942 3.365 17.655 1.00 0.00 O +ATOM 40 CB NGP A 20 23.902 2.192 18.499 1.00 0.00 B +ATOM 41 N NGP A 21 22.423 3.141 15.952 1.00 0.00 N +ATOM 42 H NGP A 21 23.206 2.686 15.519 1.00 0.00 H +ATOM 43 CA NGP A 21 21.888 4.236 15.157 1.00 0.00 C +ATOM 44 C NGP A 21 20.440 3.987 14.830 1.00 0.00 C +ATOM 45 O NGP A 21 19.685 4.899 14.971 1.00 0.00 O +ATOM 46 CB NGP A 21 22.699 4.646 13.935 1.00 0.00 B +ATOM 47 N NGP A 22 20.085 2.732 14.393 1.00 0.00 N +ATOM 48 H NGP A 22 20.695 1.997 14.279 1.00 0.00 H +ATOM 49 CA NGP A 22 18.740 2.273 14.020 1.00 0.00 C +ATOM 50 O NGP A 22 16.648 2.899 15.096 1.00 0.00 O +ATOM 51 CB NGP A 22 18.733 0.860 13.418 1.00 0.00 B +TER 52 CB NGP A 22 +END diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2/crystal_structure.fasta b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2/crystal_structure.fasta new file mode 100644 index 00000000..ecad78e0 --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2/crystal_structure.fasta @@ -0,0 +1,2 @@ +>CRYSTAL_STRUCTURE:A +PALISWIKR diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2/crystal_structure.pdb b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2/crystal_structure.pdb new file mode 100644 index 00000000..b1f527a9 --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2/crystal_structure.pdb @@ -0,0 +1,169 @@ +REMARK 1 CREATED WITH OPENMM 8.1.1, 2025-12-23 +CRYST1 60.832 38.293 42.211 90.00 90.00 90.00 P 1 1 +ATOM 1 N PRO A 14 31.689 -1.979 14.106 1.00 0.00 N +ATOM 2 H2 PRO A 14 31.276 -2.955 14.661 1.00 0.00 H +ATOM 3 H3 PRO A 14 31.802 -1.230 15.035 1.00 0.00 H +ATOM 4 CA PRO A 14 31.026 -1.278 13.030 1.00 0.00 C +ATOM 5 HA PRO A 14 31.087 -0.087 13.067 1.00 0.00 H +ATOM 6 C PRO A 14 29.521 -1.670 12.857 1.00 0.00 C +ATOM 7 O PRO A 14 28.657 -0.801 12.744 1.00 0.00 O +ATOM 8 CB PRO A 14 31.845 -1.614 11.816 1.00 0.00 C +ATOM 9 HB2 PRO A 14 31.360 -2.281 10.948 1.00 0.00 H +ATOM 10 HB3 PRO A 14 32.105 -0.652 11.150 1.00 0.00 H +ATOM 11 CG PRO A 14 33.118 -2.205 12.303 1.00 0.00 C +ATOM 12 HG2 PRO A 14 33.354 -3.243 11.750 1.00 0.00 H +ATOM 13 HG3 PRO A 14 34.080 -1.569 11.972 1.00 0.00 H +ATOM 14 CD PRO A 14 33.098 -2.363 13.769 1.00 0.00 C +ATOM 15 HD2 PRO A 14 33.941 -1.705 14.312 1.00 0.00 H +ATOM 16 HD3 PRO A 14 33.456 -3.462 14.092 1.00 0.00 H +ATOM 17 N ALA A 15 29.207 -2.952 12.868 1.00 0.00 N +ATOM 18 H ALA A 15 30.005 -3.794 12.606 1.00 0.00 H +ATOM 19 CA ALA A 15 27.822 -3.418 12.724 1.00 0.00 C +ATOM 20 HA ALA A 15 27.464 -2.944 11.690 1.00 0.00 H +ATOM 21 C ALA A 15 27.023 -3.016 13.951 1.00 0.00 C +ATOM 22 O ALA A 15 25.872 -2.551 13.769 1.00 0.00 O +ATOM 23 CB ALA A 15 27.741 -4.906 12.502 1.00 0.00 C +ATOM 24 HB1 ALA A 15 26.960 -5.122 11.612 1.00 0.00 H +ATOM 25 HB2 ALA A 15 27.299 -5.602 13.372 1.00 0.00 H +ATOM 26 HB3 ALA A 15 28.660 -5.560 12.095 1.00 0.00 H +ATOM 27 N LEU A 16 27.570 -3.117 15.127 1.00 0.00 N +ATOM 28 H LEU A 16 28.311 -4.043 15.235 1.00 0.00 H +ATOM 29 CA LEU A 16 26.958 -2.649 16.351 1.00 0.00 C +ATOM 30 HA LEU A 16 26.042 -3.413 16.370 1.00 0.00 H +ATOM 31 C LEU A 16 26.614 -1.169 16.344 1.00 0.00 C +ATOM 32 O LEU A 16 25.599 -0.734 16.933 1.00 0.00 O +ATOM 33 CB LEU A 16 27.811 -3.027 17.542 1.00 0.00 C +ATOM 34 HB2 LEU A 16 28.937 -2.668 17.356 1.00 0.00 H +ATOM 35 HB3 LEU A 16 27.935 -4.219 17.610 1.00 0.00 H +ATOM 36 CG LEU A 16 27.384 -2.550 18.921 1.00 0.00 C +ATOM 37 HG LEU A 16 27.514 -1.374 19.018 1.00 0.00 H +ATOM 38 CD1 LEU A 16 26.031 -3.234 19.257 1.00 0.00 C +ATOM 39 HD11 LEU A 16 24.991 -2.840 18.834 1.00 0.00 H +ATOM 40 HD12 LEU A 16 25.864 -3.158 20.443 1.00 0.00 H +ATOM 41 HD13 LEU A 16 25.963 -4.423 19.106 1.00 0.00 H +ATOM 42 CD2 LEU A 16 28.445 -2.970 19.933 1.00 0.00 C +ATOM 43 HD21 LEU A 16 28.316 -4.043 20.454 1.00 0.00 H +ATOM 44 HD22 LEU A 16 29.611 -3.035 19.656 1.00 0.00 H +ATOM 45 HD23 LEU A 16 28.497 -2.237 20.881 1.00 0.00 H +ATOM 46 N ILE A 17 27.514 -0.365 15.791 1.00 0.00 N +ATOM 47 H ILE A 17 28.628 -0.758 15.698 1.00 0.00 H +ATOM 48 CA ILE A 17 27.343 1.056 15.618 1.00 0.00 C +ATOM 49 HA ILE A 17 27.131 1.458 16.719 1.00 0.00 H +ATOM 50 C ILE A 17 26.081 1.392 14.758 1.00 0.00 C +ATOM 51 O ILE A 17 25.380 2.240 15.282 1.00 0.00 O +ATOM 52 CB ILE A 17 28.579 1.847 15.132 1.00 0.00 C +ATOM 53 HB ILE A 17 29.228 1.447 14.218 1.00 0.00 H +ATOM 54 CG1 ILE A 17 29.586 1.858 16.352 1.00 0.00 C +ATOM 55 HG12 ILE A 17 29.162 2.458 17.298 1.00 0.00 H +ATOM 56 HG13 ILE A 17 30.039 0.835 16.791 1.00 0.00 H +ATOM 57 CG2 ILE A 17 28.268 3.288 14.691 1.00 0.00 C +ATOM 58 HG21 ILE A 17 28.042 3.268 13.517 1.00 0.00 H +ATOM 59 HG22 ILE A 17 29.137 4.118 14.665 1.00 0.00 H +ATOM 60 HG23 ILE A 17 27.512 3.793 15.466 1.00 0.00 H +ATOM 61 CD1 ILE A 17 30.856 2.696 16.161 1.00 0.00 C +ATOM 62 HD11 ILE A 17 31.458 2.727 17.204 1.00 0.00 H +ATOM 63 HD12 ILE A 17 31.660 2.198 15.423 1.00 0.00 H +ATOM 64 HD13 ILE A 17 30.974 3.856 15.882 1.00 0.00 H +ATOM 65 N SER A 18 25.930 0.759 13.657 1.00 0.00 N +ATOM 66 H SER A 18 26.912 0.800 12.987 1.00 0.00 H +ATOM 67 CA SER A 18 24.825 0.827 12.744 1.00 0.00 C +ATOM 68 HA SER A 18 24.692 1.936 12.326 1.00 0.00 H +ATOM 69 C SER A 18 23.499 0.405 13.438 1.00 0.00 C +ATOM 70 O SER A 18 22.557 1.165 13.352 1.00 0.00 O +ATOM 71 CB SER A 18 25.076 0.039 11.491 1.00 0.00 C +ATOM 72 HB2 SER A 18 25.292 -1.128 11.323 1.00 0.00 H +ATOM 73 HB3 SER A 18 25.948 0.476 10.797 1.00 0.00 H +ATOM 74 OG SER A 18 23.902 0.046 10.670 1.00 0.00 O +ATOM 75 HG SER A 18 24.014 0.879 9.826 1.00 0.00 H +ATOM 76 N TRP A 19 23.512 -0.661 14.161 1.00 0.00 N +ATOM 77 H TRP A 19 24.036 -1.593 13.643 1.00 0.00 H +ATOM 78 CA TRP A 19 22.492 -1.085 15.081 1.00 0.00 C +ATOM 79 HA TRP A 19 21.482 -1.368 14.518 1.00 0.00 H +ATOM 80 C TRP A 19 22.083 0.004 16.012 1.00 0.00 C +ATOM 81 O TRP A 19 20.820 0.244 16.160 1.00 0.00 O +ATOM 82 CB TRP A 19 22.854 -2.410 15.767 1.00 0.00 C +ATOM 83 HB2 TRP A 19 23.060 -3.306 15.000 1.00 0.00 H +ATOM 84 HB3 TRP A 19 23.734 -2.485 16.561 1.00 0.00 H +ATOM 85 CG TRP A 19 21.803 -2.993 16.678 1.00 0.00 C +ATOM 86 CD1 TRP A 19 20.917 -3.950 16.210 1.00 0.00 C +ATOM 87 HD1 TRP A 19 21.162 -4.946 15.606 1.00 0.00 H +ATOM 88 CD2 TRP A 19 21.448 -2.745 18.041 1.00 0.00 C +ATOM 89 NE1 TRP A 19 20.060 -4.304 17.222 1.00 0.00 N +ATOM 90 HE1 TRP A 19 19.166 -5.082 17.130 1.00 0.00 H +ATOM 91 CE2 TRP A 19 20.357 -3.624 18.372 1.00 0.00 C +ATOM 92 CE3 TRP A 19 21.879 -1.892 19.048 1.00 0.00 C +ATOM 93 HE3 TRP A 19 23.012 -1.653 19.280 1.00 0.00 H +ATOM 94 CZ2 TRP A 19 19.784 -3.690 19.612 1.00 0.00 C +ATOM 95 HZ2 TRP A 19 18.893 -4.428 19.882 1.00 0.00 H +ATOM 96 CZ3 TRP A 19 21.292 -1.950 20.288 1.00 0.00 C +ATOM 97 HZ3 TRP A 19 21.593 -1.341 21.264 1.00 0.00 H +ATOM 98 CH2 TRP A 19 20.230 -2.805 20.601 1.00 0.00 C +ATOM 99 HH2 TRP A 19 19.699 -2.847 21.664 1.00 0.00 H +ATOM 100 N ILE A 20 22.930 0.594 16.823 1.00 0.00 N +ATOM 101 H ILE A 20 24.076 0.541 16.550 1.00 0.00 H +ATOM 102 CA ILE A 20 22.628 1.633 17.766 1.00 0.00 C +ATOM 103 HA ILE A 20 21.789 1.290 18.542 1.00 0.00 H +ATOM 104 C ILE A 20 21.917 2.819 17.080 1.00 0.00 C +ATOM 105 O ILE A 20 20.942 3.365 17.655 1.00 0.00 O +ATOM 106 CB ILE A 20 23.902 2.192 18.499 1.00 0.00 C +ATOM 107 HB ILE A 20 24.715 2.724 17.819 1.00 0.00 H +ATOM 108 CG1 ILE A 20 24.481 0.986 19.363 1.00 0.00 C +ATOM 109 HG12 ILE A 20 23.788 1.030 20.353 1.00 0.00 H +ATOM 110 HG13 ILE A 20 24.628 -0.201 19.461 1.00 0.00 H +ATOM 111 CG2 ILE A 20 23.599 3.421 19.390 1.00 0.00 C +ATOM 112 HG21 ILE A 20 22.661 3.366 20.137 1.00 0.00 H +ATOM 113 HG22 ILE A 20 23.360 4.447 18.810 1.00 0.00 H +ATOM 114 HG23 ILE A 20 24.460 3.891 20.098 1.00 0.00 H +ATOM 115 CD1 ILE A 20 26.033 1.304 19.637 1.00 0.00 C +ATOM 116 HD11 ILE A 20 26.619 2.239 19.171 1.00 0.00 H +ATOM 117 HD12 ILE A 20 26.965 0.585 19.850 1.00 0.00 H +ATOM 118 HD13 ILE A 20 25.915 1.670 20.777 1.00 0.00 H +ATOM 119 N LYS A 21 22.464 3.177 15.957 1.00 0.00 N +ATOM 120 H LYS A 21 23.548 2.990 15.537 1.00 0.00 H +ATOM 121 CA LYS A 21 21.888 4.236 15.157 1.00 0.00 C +ATOM 122 HA LYS A 21 21.684 5.156 15.887 1.00 0.00 H +ATOM 123 C LYS A 21 20.436 3.910 14.752 1.00 0.00 C +ATOM 124 O LYS A 21 19.685 4.899 14.971 1.00 0.00 O +ATOM 125 CB LYS A 21 22.699 4.646 13.935 1.00 0.00 C +ATOM 126 HB2 LYS A 21 21.993 5.432 13.366 1.00 0.00 H +ATOM 127 HB3 LYS A 21 22.859 3.879 13.036 1.00 0.00 H +ATOM 128 CG LYS A 21 23.944 5.416 14.471 1.00 0.00 C +ATOM 129 HG2 LYS A 21 23.539 6.515 14.726 1.00 0.00 H +ATOM 130 HG3 LYS A 21 24.475 5.169 15.505 1.00 0.00 H +ATOM 131 CD LYS A 21 24.919 5.669 13.300 1.00 0.00 C +ATOM 132 HD2 LYS A 21 24.419 6.421 12.513 1.00 0.00 H +ATOM 133 HD3 LYS A 21 25.267 4.750 12.623 1.00 0.00 H +ATOM 134 CE LYS A 21 26.173 6.287 13.908 1.00 0.00 C +ATOM 135 HE2 LYS A 21 25.834 7.406 14.184 1.00 0.00 H +ATOM 136 HE3 LYS A 21 26.807 6.035 14.888 1.00 0.00 H +ATOM 137 NZ LYS A 21 27.199 6.564 12.863 1.00 0.00 N +ATOM 138 HZ1 LYS A 21 26.833 7.125 11.866 1.00 0.00 H +ATOM 139 HZ2 LYS A 21 27.890 5.710 12.384 1.00 0.00 H +ATOM 140 HZ3 LYS A 21 28.009 7.353 13.267 1.00 0.00 H +ATOM 141 N ARG A 22 20.075 2.728 14.351 1.00 0.00 N +ATOM 142 H ARG A 22 20.875 1.866 14.278 1.00 0.00 H +ATOM 143 CA ARG A 22 18.740 2.273 14.020 1.00 0.00 C +ATOM 144 HA ARG A 22 18.281 3.145 13.343 1.00 0.00 H +ATOM 145 C ARG A 22 17.807 2.365 15.177 1.00 0.00 C +ATOM 146 O ARG A 22 16.648 2.899 15.096 1.00 0.00 O +ATOM 147 CB ARG A 22 18.733 0.860 13.418 1.00 0.00 C +ATOM 148 HB2 ARG A 22 18.954 -0.058 14.146 1.00 0.00 H +ATOM 149 HB3 ARG A 22 17.556 0.698 13.252 1.00 0.00 H +ATOM 150 CG ARG A 22 19.309 0.956 12.004 1.00 0.00 C +ATOM 151 HG2 ARG A 22 18.649 1.739 11.375 1.00 0.00 H +ATOM 152 HG3 ARG A 22 20.397 1.373 11.744 1.00 0.00 H +ATOM 153 CD ARG A 22 19.117 -0.300 11.254 1.00 0.00 C +ATOM 154 HD2 ARG A 22 19.518 -0.186 10.130 1.00 0.00 H +ATOM 155 HD3 ARG A 22 17.968 -0.467 10.943 1.00 0.00 H +ATOM 156 NE ARG A 22 19.382 -1.562 11.991 1.00 0.00 N +ATOM 157 HE ARG A 22 18.475 -2.310 12.190 1.00 0.00 H +ATOM 158 CZ ARG A 22 20.624 -2.104 11.889 1.00 0.00 C +ATOM 159 NH1 ARG A 22 21.664 -1.554 11.252 1.00 0.00 N +ATOM 160 HH11 ARG A 22 21.542 -1.383 10.077 1.00 0.00 H +ATOM 161 HH12 ARG A 22 22.689 -2.158 11.323 1.00 0.00 H +ATOM 162 NH2 ARG A 22 20.870 -3.271 12.498 1.00 0.00 N +ATOM 163 HH21 ARG A 22 20.997 -4.155 11.703 1.00 0.00 H +ATOM 164 HH22 ARG A 22 20.378 -3.797 13.442 1.00 0.00 H +ATOM 165 OXT ARG A 22 18.610 1.777 15.932 1.00 0.00 O +TER 166 ARG A 22 +END diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2/forces_setup.py b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2/forces_setup.py new file mode 100644 index 00000000..49f5b654 --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2/forces_setup.py @@ -0,0 +1,46 @@ +from openawsem.functionTerms import * +from openawsem.helperFunctions.myFunctions import * + +try: + from openmm.unit import angstrom + from openmm.unit import kilocalorie_per_mole +except ModuleNotFoundError: + from simtk.unit import angstrom + from simtk.unit import kilocalorie_per_mole + +def set_up_forces(oa, computeQ=False, submode=-1, contactParameterLocation=".", membrane_center=-0*angstrom): + # apply forces + forces = [ + basicTerms.con_term(oa), + basicTerms.chain_term(oa), + basicTerms.chi_term(oa), + basicTerms.excl_term(oa), + basicTerms.rama_term(oa), + basicTerms.rama_proline_term(oa), + basicTerms.rama_ssweight_term(oa, k_rama_ssweight=2*8.368), + contactTerms.contact_term(oa), + # for membrane protein simulation use contact_term below. + # contact_term(oa, z_dependent=True, inMembrane=True, membrane_center=membrane_center, k_relative_mem=3), + hydrogenBondTerms.beta_term_1(oa), + hydrogenBondTerms.beta_term_2(oa), + hydrogenBondTerms.beta_term_3(oa), + hydrogenBondTerms.pap_term_1(oa), + hydrogenBondTerms.pap_term_2(oa), + # membraneTerms.membrane_term(oa, k=1*kilocalorie_per_mole, membrane_center=membrane_center), + # membraneTerms.membrane_preassigned_term(oa, k=1*kilocalorie_per_mole, membrane_center=membrane_center, zimFile="PredictedZim"), + # templateTerms.er_term(oa), + # templateTerms.fragment_memory_term(oa, frag_file_list_file="./frags.mem", npy_frag_table="./frags.npy", UseSavedFragTable=True), + templateTerms.fragment_memory_term(oa, frag_file_list_file="./single_frags.mem", npy_frag_table="./single_frags.npy", UseSavedFragTable=False), + debyeHuckelTerms.debye_huckel_term(oa, chargeFile="charge.txt"), + ] + if computeQ: + forces.append(biasTerms.rg_term(oa)) + forces.append(biasTerms.q_value(oa, "crystal_structure-cleaned.pdb", forceGroup=1)) + forces.append(biasTerms.qc_value(oa, "crystal_structure-cleaned.pdb")) + # forces.append(partial_q_value(oa, "crystal_structure-cleaned.pdb", residueIndexGroup=list(range(0, 15)), forceGroup=1)) + if submode == 0: + additional_forces = [ + # contact_term(oa), + ] + forces += additional_forces + return forces diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2/gamma.dat b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2/gamma.dat new file mode 100644 index 00000000..ebe8e61b --- /dev/null +++ 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+-0.45560 -1.49440 diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2/mm_analyze.py b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2/mm_analyze.py new file mode 100755 index 00000000..4a4ca638 --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2/mm_analyze.py @@ -0,0 +1,210 @@ +#!/usr/bin/env python3 +import os +import argparse +import sys +from time import sleep +import subprocess +import fileinput +import platform +import importlib.util + +# __location__ = os.path.realpath(os.path.join(os.getcwd(), os.path.dirname(__file__))) +# __author__ = 'Wei Lu' + +from openawsem import * +from openawsem.helperFunctions.myFunctions import * + +def analyze(args): + if (args.debug): + do = print + cd = print + else: + do = os.system + cd = os.chdir + + # if mm_run.py is not at the same location of your setup folder. + setupFolderPath = os.path.dirname(args.protein) + setupFolderPath = "." if setupFolderPath == "" else setupFolderPath + proteinName = pdb_id = os.path.basename(args.protein) + chain=args.chain + pdb = f"{pdb_id}.pdb" + + trajectoryPath = os.path.abspath(args.trajectory) + if args.output is None: + outFile = os.path.join(os.path.dirname(trajectoryPath), "info.dat") + else: + outFile = os.path.join(os.path.dirname(trajectoryPath), args.output) + + forceSetupFile = None if args.forces is None else os.path.abspath(args.forces) + parametersLocation = "." if args.parameters is None else os.path.abspath(args.parameters) + os.chdir(setupFolderPath) + + simulation_platform = args.platform + platform = Platform.getPlatformByName(simulation_platform) + if simulation_platform == "CPU": + if args.thread != -1: + platform.setPropertyDefaultValue("Threads", str(args.thread)) + print(f"{simulation_platform}: {platform.getPropertyDefaultValue('Threads')} threads") + + + + if chain == "-1": + chain = getAllChains("crystal_structure.pdb") + print("Chains to simulate: ", chain) + + # for compute Q + if args.fromOpenMMPDB: + input_pdb_filename = proteinName + seq=read_fasta("crystal_structure.fasta") + print(f"Using Seq:\n{seq}") + else: + suffix = '-openmmawsem.pdb' + if pdb_id[-len(suffix):] == suffix: + input_pdb_filename = pdb_id + else: + input_pdb_filename = f"{pdb_id}-openmmawsem.pdb" + seq=None + + if args.fasta == "": + seq = None + else: + seq = seq=read_fasta(args.fasta) + print(f"Using Seq:\n{seq}") + + fileType = trajectoryPath[-3:] + if fileType == "pdb": + pdb_trajectory = md.load(trajectoryPath, stride=1) + elif fileType == "dcd": + pdb_trajectory = md.load(trajectoryPath, top=input_pdb_filename, stride=1) + # may use iterload if loading still too slow + else: + print(f"Unknown fileType {fileType}") + # pdb_trajectory = read_trajectory_pdb_positions(trajectoryPath) + + # check for atoms whose positions are intended to be fixed + if args.fixed_residue_indices: + with open(args.fixed_residue_indices,'r') as f: + for line in f: # only expect 1 line + fixed_residue_indices = line.strip().split(',') #expecting a one-line csv + fixed_residue_indices = [int(item) for item in fixed_residue_indices] + break + else: + fixed_residue_indices = [] + + oa = OpenMMAWSEMSystem(input_pdb_filename, chains=chain, k_awsem=1.0, xml_filename=openawsem.xml, seqFromPdb=seq, + fixed_residue_indices=fixed_residue_indices,periodic_box=args.periodic_box, + includeLigands=args.includeLigands) # k_awsem is an overall scaling factor that will affect the relevant temperature scales + + print(f"using force setup file from {forceSetupFile}") + spec = importlib.util.spec_from_file_location("forces", forceSetupFile) + # print(spec) + forces = importlib.util.module_from_spec(spec) + spec.loader.exec_module(forces) + forces = forces.set_up_forces(oa, computeQ=True, submode=args.subMode, contactParameterLocation=parametersLocation) + oa.addForcesWithDefaultForceGroup(forces) + # print(forces) + + # start simulation + collision_rate = 5.0 / picoseconds + + integrator = LangevinIntegrator(300*kelvin, 1/picosecond, 2*femtoseconds) + simulation = Simulation(oa.pdb.topology, oa.system, integrator, platform) + + # apply forces + forceGroupTable = {"Backbone":20, "Rama":21, "Contact":22, "Fragment":23, "Membrane":24, "ER":25, "TBM_Q":26, "Beta":27, "Pap":28, "Helical":29, + "Q":1, "Rg":2, "Qc":3, + "Helix_orientation":18, "Pulling":19, "Debye_huckel":30, + "Total":list(range(11, 32)) + # , "Q_wat":4, "Q_mem":5, + } + print("Please ensure the forceGroupTable in mm_analysis is set up correctly if you are adding new energy terms.") + print("Also, please notice that the total energy include all the terms with group index range from 11 to 32.") + # forceGroupTable = {"Con":11, "Chain":12, "Chi":13, "Excluded":14, "Rama":15, "Direct":16, + # "Burial":17, "Mediated":18, "Contact":18, "Fragment":19, "Membrane":20, "ER":21,"TBM_Q":22, "beta_1":23, "beta_2":24,"beta_3":25,"pap":26, "Total":list(range(11, 32)), + # "Water":[16, 18], "Beta":[23, 24, 25], "Pap":26, "Rg_Bias":27, "Helical":28, "Pulling":29, "Q":1, "Rg":2, "Qc":3, "Q_wat":4, "Q_mem":5} + # forceGroupTable_Rev = {11:"Con", 12:"Chain", 13:"Chi", 14:"Excluded", 15:"Rama", 16:"Direct", + # 17:"Burial", 18:"Mediated", 19:"Fragment"} + # forceGroupTable = {"Con":11, "Chain":12, "Chi":13, "Excluded":14, "Rama":15, "Direct":16, + # "Burial":17, "Mediated":18, "Contact":18, "Fragment":19, "Membrane":20, "ER":21,"TBM_Q":22, "beta_1":23, "beta_2":24,"beta_3":25,"pap":26, "Total":list(range(11, 27)), + # "Water":[16, 18], "Beta":[23, 24, 25], "Pap":26, "Q":1} + # forceGroupTable = {"Con":11, "Chain":12, "Chi":13, "Excluded":14, "Rama":15, "Direct":16, + # "Burial":17, "Mediated":18, "Contact":18, "Fragment":19, "Membrane":20, "ER":21,"TBM_Q":22, "beta_1":23, "Total":list(range(11, 26)), + # "Water":[16, 18], "beta":[23, 24, 25], "Q":1} + showValue = ["Q", "Qc", "Rg"] + # term in showEnergy will assume to take on the energy unit of kilojoule_per_mole, it will be shown in unit of kilocalories_per_mole(divided by 4.184) + # term in showValue will not be converted. + showEnergy = ["Backbone", "Rama", "Contact", "Fragment", "Membrane", "ER", "TBM_Q", "Beta", "Pap", "Helical", "Debye_huckel","Total"] + showAll = showValue + showEnergy + # , "Disulfide" + # showEnergy = ["Q", "Qc", "Rg", "Con", "Chain", "Chi", "Excluded", "Rama", "Contact", "Helical", "Fragment", "Membrane", "ER", "Beta", "Pap", "Total"] + # showEnergy = ["Q", "Qc", "Rg", "Pulling", "Con", "Chain", "Chi", "Excluded", "Rama", "Contact", "FamilyFold", "Fragment", "Membrane", "Beta", "Pap", "Rg_Bias", "Total"] + # showEnergy = ["Q", "Con", "Chain", "Chi", "Excluded", "Rama", "Contact", "Fragment", "Membrane", "Beta", "Pap", "Total"] + # showEnergy = ["Q", "Con", "Chain", "Chi", "Excluded", "Rama", "Contact", "Fragment", "Membrane", "Total"] + # showEnergy = ["Q", "Con", "Chain", "Chi", "Excluded", "Rama", "Contact", "Fragment", "Membrane","ER","TBM_Q","beta_1", "Total"] + # showEnergy = ["Q", "Con", "Chain", "Chi", "Excluded", "Rama", "Contact", "Fragment", "Membrane","ER","TBM_Q","beta_1","beta_2","beta_3","pap", "Total"] + # print("Steps", *showEnergy) + print("Printing energies") + + with open(outFile, "w") as out: + line = " ".join(["{0:<8s}".format(i) for i in ["Steps"] + showAll]) + print(line) + out.write(line+"\n") + # for step, pdb in enumerate(pdb_trajectory): + # simulation.context.setPositions(pdb.positions) + for step in range(len(pdb_trajectory)): + simulation.context.setPositions(pdb_trajectory.openmm_positions(step)) + e = [] + for term in showAll: + if type(forceGroupTable[term]) == list: + g = set(forceGroupTable[term]) + elif forceGroupTable[term] == -1: + g = -1 + else: + g = {forceGroupTable[term]} + state = simulation.context.getState(getEnergy=True, groups=g) + # if term == "Q" or term == "Rg" or term == "Qc" or term == "Q_wat" or term == "Q_mem": + if term in showValue: + termEnergy = state.getPotentialEnergy().value_in_unit(kilojoule_per_mole) + else: + termEnergy = state.getPotentialEnergy().value_in_unit(kilocalories_per_mole) + e.append(termEnergy) + # print(*e) + line = " ".join([f"{step:<8}"] + ["{0:<8.2f}".format(i) for i in e]) + print(line) + out.write(line+"\n") + # print(forceGroupTable[term], state.getPotentialEnergy().value_in_unit(kilocalories_per_mole)) + +def main(args=None): + parser = argparse.ArgumentParser( + description="The goal of this python3 code is to automatically create \ + the project template as fast as possible. Written by Wei Lu." + ) + parser.add_argument("protein", help="The name of the protein") + parser.add_argument("-d", "--debug", action="store_true", default=False) + parser.add_argument("-c", "--chain", type=str, default="-1") + parser.add_argument("--thread", type=int, default=2, help="default is using 2 CPUs, -1 is using all") + parser.add_argument("-p", "--platform", type=str, default="CPU", help="Could be OpenCL, CUDA and CPU") + parser.add_argument("-t", "--trajectory", type=str, default="./movie.pdb") + parser.add_argument("-o", "--output", type=str, default=None, help="The Name of file that shows your energy and Q information.") + parser.add_argument("--subMode", type=int, default=3) + parser.add_argument("-f", "--forces", default="forces_setup.py") + parser.add_argument("--parameters", default=None) + parser.add_argument("--fromOpenMMPDB", action="store_true", default=False) + parser.add_argument("--fasta", type=str, default="crystal_structure.fasta") + parser.add_argument("--includeLigands", action="store_true", default=False) + parser.add_argument('--periodic_box', type=float, nargs=3, metavar=('X', 'Y', 'Z'), help='Enable periodic boundary conditions with box dimensions in x, y, z (nanometers)') + parser.add_argument('--fixed_residue_indices', type=str, default='', help='csv file with indices (not "ids" or "resnums") of residues whose positions should be fixed)') + + if args is None: + args = parser.parse_args() + else: + args = parser.parse_args(args) + + with open('analysis_commandline_args.txt', 'a') as f: + f.write(' '.join(sys.argv)) + f.write('\n') + print(' '.join(sys.argv)) + analyze(args) + +if __name__=="__main__": + main() diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2/mm_run.py b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2/mm_run.py new file mode 100755 index 00000000..ad3064b4 --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2/mm_run.py @@ -0,0 +1,377 @@ +#!/usr/bin/env python3 +import os +import sys +import time +import argparse +import importlib.util + +from openawsem import * +from openawsem.helperFunctions.myFunctions import * + +do = os.system +cd = os.chdir + +def run(args): + simulation_platform = args.platform + platform = Platform.getPlatformByName(simulation_platform) + if simulation_platform == "CPU": + if args.thread != -1: + platform.setPropertyDefaultValue("Threads", str(args.thread)) + print(f"{simulation_platform}: {platform.getPropertyDefaultValue('Threads')} threads") + elif simulation_platform=="OpenCL": + platform.setPropertyDefaultValue('OpenCLPlatformIndex', '0') + platform.setPropertyDefaultValue('DeviceIndex', str(args.device)) + elif simulation_platform=="CUDA": + platform.setPropertyDefaultValue('DeviceIndex', str(args.device)) + + # if mm_run.py is not at the same location of your setup folder. + setupFolderPath = os.path.dirname(args.protein) + setupFolderPath = "." if setupFolderPath == "" else setupFolderPath + proteinName = pdb_id = os.path.basename(args.protein) + + pwd = os.getcwd() + toPath = os.path.abspath(args.to) + checkPointPath = None if args.fromCheckPoint is None else os.path.abspath(args.fromCheckPoint) + forceSetupFile = None if args.forces is None else os.path.abspath(args.forces) + parametersLocation = "." if args.parameters is None else os.path.abspath(args.parameters) + os.chdir(setupFolderPath) + + + + # chain=args.chain + chain=args.chain + pdb = f"{pdb_id}.pdb" + + if chain == "-1": + chain = getAllChains("crystal_structure.pdb") + print("Chains to simulate: ", chain) + + + if args.to != "./": + # os.system(f"mkdir -p {args.to}") + os.makedirs(toPath, exist_ok=True) + os.system(f"cp {forceSetupFile} {toPath}/forces_setup.py") + os.system(f"cp crystal_structure.fasta {toPath}/") + os.system(f"cp crystal_structure.pdb {toPath}/") + # os.system(f"cp {pdb} {args.to}/{pdb}") + # pdb = os.path.join(args.to, pdb) + + if args.fromOpenMMPDB: + input_pdb_filename = proteinName + seq=read_fasta("crystal_structure.fasta") + print(f"Using Seq:\n{seq}") + else: + suffix = '-openmmawsem.pdb' + if pdb_id[-len(suffix):] == suffix: + input_pdb_filename = pdb_id + else: + input_pdb_filename = f"{pdb_id}-openmmawsem.pdb" + seq=None + + if args.fasta == "": + seq = None + else: + seq = seq=read_fasta(args.fasta) + print(f"Using Seq:\n{seq}") + # start simulation + collision_rate = 5.0 / picoseconds + + # check for atoms whose positions are intended to be fixed + if args.fixed_residue_indices: + with open(args.fixed_residue_indices,'r') as f: + for line in f: # only expect 1 line + fixed_residue_indices = line.strip().split(',') #expecting a one-line csv + fixed_residue_indices = [int(item) for item in fixed_residue_indices] + break + else: + fixed_residue_indices = [] + + # assign annealing parameters + Tstart = args.tempStart + Tend = args.tempEnd + + print(f"using force setup file from {forceSetupFile}") + spec = importlib.util.spec_from_file_location("forces", forceSetupFile) + # print(spec) + forces = importlib.util.module_from_spec(spec) + spec.loader.exec_module(forces) + + + oa = OpenMMAWSEMSystem(input_pdb_filename, k_awsem=1.0, chains=chain, xml_filename=openawsem.xml, seqFromPdb=seq, + includeLigands=args.includeLigands, periodic_box=args.periodic_box, + fixed_residue_indices=fixed_residue_indices) # k_awsem is an overall scaling factor that will affect the relevant temperature scales + myForces = forces.set_up_forces(oa, submode=args.subMode, contactParameterLocation=parametersLocation,) + # print(forces) + # oa.addForces(myForces) + + if args.removeCMMotionRemover: + oa.system.removeForce(0) + oa.addForcesWithDefaultForceGroup(myForces) + + #Define output paths + output_path = os.path.join(toPath, "output.log") + native_pdb_path = os.path.join(toPath, "native.pdb") + movie_pdb_path = os.path.join(toPath, "movie.pdb") + movie_dcd_path = os.path.join(toPath, "movie.dcd") + time_dat_path = os.path.join(toPath, "time.dat") + info_dat_path = os.path.join(toPath, "info.dat") + checkpoint_path = os.path.join(toPath, args.checkpointFile) + + if args.fromCheckPoint: + integrator = LangevinIntegrator(Tstart*kelvin, 1/picosecond, args.timeStep*femtoseconds) + simulation = Simulation(oa.pdb.topology, oa.system, integrator, platform) + simulation.loadCheckpoint(checkPointPath) + reporter_append = True + else: + # output the native and the structure after minimization + integrator = CustomIntegrator(0.001) + simulation = Simulation(oa.pdb.topology, oa.system, integrator, platform) + simulation.context.setPositions(oa.pdb.positions) # set the initial positions of the atoms + + simulation.reporters.append(PDBReporter(native_pdb_path, 1)) + simulation.reporters.append(DCDReporter(movie_dcd_path, 1)) + + simulation.step(int(1)) + simulation.minimizeEnergy() # first, minimize the energy to a local minimum to reduce any large forces that might be present + simulation.step(int(1)) + reporter_append = False + + + # print("------------------Folding-------------------") + # oa = OpenMMAWSEMSystem(input_pdb_filename, k_awsem=1.0, chains=chain, xml_filename=OPENAWSEM_LOCATION+"awsem.xml") # k_awsem is an overall scaling factor that will affect the relevant temperature scales + # myForces = forces.set_up_forces(oa, submode=args.subMode, contactParameterLocation=parametersLocation) + # oa.addForces(myForces) + + integrator = LangevinIntegrator(Tstart*kelvin, 1/picosecond, args.timeStep*femtoseconds) + # integrator.setRandomNumberSeed(A_NUMBER_AS_RANDOM_SEED) + # integrator = CustomIntegrator(0.001) + simulation = Simulation(oa.pdb.topology, oa.system, integrator, platform) + # simulation.loadState(os.path.join(toPath, 'output.xml')) + simulation.context.setPositions(oa.pdb.positions) # set the initial positions of the atoms + simulation.context.setVelocitiesToTemperature(Tstart*kelvin) # set the initial velocities of the atoms according to the desired starting temperature + # simulation.context.setVelocitiesToTemperature(Tstart*kelvin, A_RANDOM_SEED_NUMBER) + simulation.minimizeEnergy() # first, minimize the energy to a local minimum to reduce any large forces that might be present + + + print("report_interval", args.reportInterval) + print("num_frames", args.numFrames) + + # Backup existing files + if reporter_append: + # Only backup checkpoint if it exists + if os.path.exists(checkpoint_path): + past_chk_dir = os.path.join(toPath, "past_checkpoints") + os.makedirs(past_chk_dir, exist_ok=True) + backup_counter = 0 + for i in range(1000): + backup_chk = os.path.join(past_chk_dir, f"checkpoint_used_{backup_counter:03d}.chk") + if not os.path.exists(backup_chk): + break + if i == 999: + raise RuntimeError("Too many used checkpoint files.") + backup_counter += 1 + # Backup checkpoint + print(f"Making backup for used checkpoint file past_checkpoints/checkpoint_used_{backup_counter:03d}.chk") + os.system(f"cp {checkpoint_path} {backup_chk}") + else: + # Ensure backup directory exists + backup_dir = os.path.join(toPath, "backup") + os.makedirs(backup_dir, exist_ok=True) + # Define files to backup: (source_path, backup_prefix, description) + files_to_backup = [ + (output_path, "output", "log file"), + (movie_dcd_path, "movie", "dcd file"), + (checkpoint_path, "checkpoint", "checkpoint file"), + (info_dat_path, "info", "info file"), + (time_dat_path, "time", "time file") + ] + + # Find the next available backup number + backup_counter = 0 + for i in range(1000): + backup_paths = [os.path.join(backup_dir, f"{prefix}_{backup_counter:03d}.{ext}") + for _, prefix, _ in files_to_backup + for ext in (['log'] if prefix == 'output' else + ['dcd'] if prefix == 'movie' else + ['chk'] if prefix == 'checkpoint' else ['dat'])] + if not any(os.path.exists(path) for path in backup_paths): + break + if i == 999: + raise RuntimeError("Too many backup files.") + backup_counter += 1 + + # Backup all files + for source_path, prefix, description in files_to_backup: + if os.path.exists(source_path): + ext = 'log' if prefix == 'output' else 'dcd' if prefix == 'movie' else 'chk' if prefix == 'checkpoint' else 'dat' + backup_path = os.path.join(backup_dir, f"{prefix}_{backup_counter:03d}.{ext}") + print(f"Making backup {description} backup/{prefix}_{backup_counter:03d}.{ext}") + os.system(f"cp {source_path} {backup_path}") + + + simulation.reporters.append(StateDataReporter(sys.stdout, args.reportInterval, step=True, potentialEnergy=True, temperature=True, append=reporter_append)) # output energy and temperature during simulation to terminal + simulation.reporters.append(StateDataReporter(output_path, args.reportInterval, step=True, potentialEnergy=True, temperature=True, append=reporter_append)) # output energy and temperature to a file + simulation.reporters.append(PDBReporter(movie_pdb_path, reportInterval=args.reportInterval)) # output PDBs of simulated structures; deprecated (see https://github.com/cabb99/openawsem/issues/86) + simulation.reporters.append(DCDReporter(movie_dcd_path, reportInterval=args.reportInterval, append=True)) # output PDBs of simulated structures. DCD is appending to the minimization output if it exists + simulation.reporters.append(CheckpointReporter(checkpoint_path, args.checkpointInterval)) # save progress during the simulation + + if args.dryRun: + if args.simulation_mode == 1: # test temperature setting + deltaT = (Tend - Tstart) / args.numFrames + for i in range(args.numFrames): + integrator.setTemperature((Tstart + deltaT*i)*kelvin) + raise SystemExit("Simulation configured successfully") + + print("Simulation Starts") + start_time = time.time() + + if args.simulation_mode == 0: + simulation.step(int(args.steps)) + elif args.simulation_mode == 1: + deltaT = (Tend - Tstart) / args.numFrames + for i in range(args.numFrames): + integrator.setTemperature((Tstart + deltaT*i)*kelvin) + simulation.step(args.reportInterval) + + # simulation.saveCheckpoint('step_%d.chk' % i) + # simulation.context.setParameter("k_membrane", 0) + # if i < snapShotCount/2: + # simulation.context.setParameter("k_membrane", (i % 2) * k_mem) + # simulation.context.setParameter("k_single_helix_orientation_bias", (i % 2) * k_single_helix_orientation_bias) + # else: + # simulation.context.setParameter("k_membrane", k_mem) + # simulation.context.setParameter("k_single_helix_orientation_bias", k_single_helix_orientation_bias) + + # simulation.context.setParameter("k_membrane", (i)*(k_mem/snapShotCount)) + # simulation.context.setParameter("k_single_helix_orientation_bias", (i)*(k_single_helix_orientation_bias/snapShotCount)) + # print(simulation.context.getParameter("k_membrane")) + + + # simulation.step(int(1e6)) + + time_taken = time.time() - start_time # time_taken is in seconds + hours, rest = divmod(time_taken,3600) + minutes, seconds = divmod(rest, 60) + print(f"---{hours} hours {minutes} minutes {seconds} seconds ---") + + with open(time_dat_path, "w") as out: + out.write(str(time_taken)+"\n") + + # accompany with analysis run + simulation = None + time.sleep(10) + os.chdir(pwd) + print(os.getcwd()) + if args.fasta == "": + analysis_fasta = "" + else: + analysis_fasta = f"--fasta {args.fasta}" + additional_cmd = "" + if args.includeLigands: + additional_cmd += "--includeLigands " + if args.periodic_box: + additional_cmd += f"--periodic_box {' '.join(map(str, args.periodic_box))} " + if args.fixed_residue_indices: + additional_cmd += f"--fixed_residue_indices {fixed_residue_indices} " + if args.fromOpenMMPDB: + additional_cmd += f"--fromOpenMMPDB " + os.system(f"{sys.executable} mm_analyze.py {args.protein} -t {os.path.join(toPath, 'movie.dcd')} --subMode {args.subMode} -f {args.forces} {analysis_fasta} {additional_cmd} -c {chain} --output {info_dat_path}") + + + + +def main(args=None): + parser = argparse.ArgumentParser( + description="This is a python3 script to automatically copy the template file and run simulations") + # default=False with action="store_true" is redundant but doesn't hurt us + parser.add_argument("protein", help="The name of the protein") + parser.add_argument("--name", default="simulation", help="Name of the simulation") + parser.add_argument("--to", default="./", help="location of movie file") + parser.add_argument("-c", "--chain", type=str, default="-1") + parser.add_argument("-t", "--thread", type=int, default=-1, help="default is using all that is available") + parser.add_argument("-p", "--platform", type=str, default="OpenCL", choices=["OpenCL", "CPU", "HIP", "Reference", "CUDA"], help="Platform to run the simulation.") + parser.add_argument("-s", "--steps", type=float, default=1e7, help="step size, default 1e7") + parser.add_argument("--tempStart", type=float, default=800, help="Starting temperature") + parser.add_argument("--tempEnd", type=float, default=200, help="Ending temperature") + parser.add_argument("--fromCheckPoint", type=str, default=None, help="The checkpoint file you want to start from") + parser.add_argument("-m", "--simulation_mode", type=int, default=1, + help="default 1,\ + 0: constant temperature,\ + 1: temperature annealing") + parser.add_argument("--subMode", type=int, default=-1) + parser.add_argument("-f", "--forces", default="forces_setup.py") + parser.add_argument("--parameters", default=None) + parser.add_argument("-r", "--reportInterval", "--reportFrequency", type=float, default=None, help="Number of steps between each frame recorded") + parser.add_argument("--checkpointInterval", type=float, default=None, help="Number of steps between each frame recorded") + parser.add_argument("--checkpointFile", type=str, default="checkpoint.chk", help="Name of the checkpoint file") + parser.add_argument("--numFrames", type=int, default=400, help="Number of frames to record. Can be overridden by --reportInterval") + parser.add_argument("--fromOpenMMPDB", action="store_true", default=False) + parser.add_argument("--fasta", type=str, default="crystal_structure.fasta") + parser.add_argument("--timeStep", type=int, default=2, help="time step in femtoseconds") + parser.add_argument("--includeLigands", action="store_true", default=False) + parser.add_argument('--device', default=0, help='OpenCL/CUDA device index') + parser.add_argument('--removeCMMotionRemover', action="store_true", default=False, help='Removes CMMotionRemover. Recommended for periodic boundary conditions and membrane simulations') + parser.add_argument('--fixed_residue_indices', type=str, default='', help='csv file with indices (not "ids" or "resnums") of residues whose positions should be fixed)') + parser.add_argument('--periodic_box', type=float, nargs=3, metavar=('X', 'Y', 'Z'), help='Enable periodic boundary conditions with box dimensions in x, y, z (nanometers)') + parser.add_argument('--dryRun',action="store_true",default=False,help="Return the configuration and exit without running the simulation") + + if args is None: + args = parser.parse_args() + else: + args = parser.parse_args(args) + + with open('commandline_args.txt', 'a') as f: + f.write(' '.join(sys.argv)) + f.write('\n') + print(' '.join(sys.argv)) + + # Correct number of timesteps if negative + if args.steps <= 0: + logging.warning("--steps must be a positive integer. Reverting to default 1e7") + args.steps = 1e7 + else: + # Convert steps to integer + args.steps = int(args.steps) + + # Adds a deprecation warning if the deprecated option '--reportFrequency' is used + if '--reportFrequency' in sys.argv: + logging.warning("The '--reportFrequency' option is deprecated. Please use '--reportInterval' instead.", DeprecationWarning) + + if args.reportInterval is None and args.numFrames>0: + #Report interval is not specified and number of frames is reasonable + if args.numFrames > args.steps: + logging.warning("Number of frames --numFrames is more than number of steps. Setting number of frames to {args.steps}.") + args.numFrames = args.steps + + args.reportInterval = math.ceil(args.steps / args.numFrames) + new_steps = int(args.reportInterval * args.numFrames) + if new_steps != args.steps: + logging.warning(f"Number of frames --reportInterval does not divide number of steps --steps exactly. Adjusting number of steps from {args.steps} to {new_steps}") + args.steps = new_steps + elif args.reportInterval is not None and args.reportInterval > 0: + #Report interval is specified and is reasonable + if '--numFrames' in sys.argv: + logging.warning("Ignoring user-specified --numFrames. --reportInterval takes priority over --numFrames. ") + args.numFrames = math.ceil(args.steps / args.reportInterval) + new_steps = int(args.numFrames * args.reportInterval) + if new_steps != args.steps: + logging.warning(f"Number of frames --numFrames does not divide number of steps --steps exactly. Adjusting number of steps from {args.steps} to {new_steps}") + args.steps = new_steps + elif args.numFrames == 0 and args.reportInterval is None: + logging.info("No frames will be recorded. Simulation will run for the specified number of steps.") + else: + logging.error("Invalid values: Either --reportInterval or --numFrames must be provided with positive values.") + raise ValueError("Both --reportInterval and --numFrames cannot be missing or zero. Please provide valid inputs.") + + args.reportInterval = int(args.reportInterval) + args.checkpointInterval = args.reportInterval if args.checkpointInterval is None else int(args.checkpointInterval) + + if args.dryRun: + print("Dry run mode. Simulation will not run.") + print(args) + return args + + run(args) + +if __name__=="__main__": + main() diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2/original_pdbs/2mlt_frag2.pdb b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2/original_pdbs/2mlt_frag2.pdb new file mode 100644 index 00000000..6673da8e --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2/original_pdbs/2mlt_frag2.pdb @@ -0,0 +1,87 @@ +CRYST1 60.832 38.293 42.211 90.00 90.00 90.00 C 2 2 21 16 +ORIGX1 1.000000 0.000000 0.000000 0.00000 +ORIGX2 0.000000 1.000000 0.000000 0.00000 +ORIGX3 0.000000 0.000000 1.000000 0.00000 +SCALE1 0.016439 0.000000 0.000000 0.00000 +SCALE2 0.000000 0.026114 0.000000 0.00000 +SCALE3 0.000000 0.000000 0.023691 0.00000 +MTRIX1 1 -0.996310 -0.033870 -0.078870 71.25100 1 +MTRIX2 1 0.048050 -0.981470 -0.185470 2.71100 1 +MTRIX3 1 -0.071130 -0.188580 0.979480 2.05300 1 +ATOM 87 N PRO A 14 31.689 -1.979 14.106 1.00 17.38 N +ATOM 88 CA PRO A 14 31.026 -1.278 13.030 1.00 17.52 C +ATOM 89 C PRO A 14 29.521 -1.670 12.857 1.00 18.98 C +ATOM 90 O PRO A 14 28.657 -0.801 12.744 1.00 16.75 O +ATOM 91 CB PRO A 14 31.845 -1.614 11.816 1.00 17.80 C +ATOM 92 CG PRO A 14 33.118 -2.205 12.303 1.00 18.05 C +ATOM 93 CD PRO A 14 33.098 -2.363 13.769 1.00 17.96 C +ATOM 94 N ALA A 15 29.207 -2.952 12.868 1.00 16.39 N +ATOM 95 CA ALA A 15 27.822 -3.418 12.724 1.00 17.10 C +ATOM 96 C ALA A 15 27.023 -3.016 13.951 1.00 16.98 C +ATOM 97 O ALA A 15 25.872 -2.551 13.769 1.00 16.78 O +ATOM 98 CB ALA A 15 27.741 -4.906 12.502 1.00 19.58 C +ATOM 99 N LEU A 16 27.570 -3.117 15.127 1.00 15.97 N +ATOM 100 CA LEU A 16 26.958 -2.649 16.351 1.00 18.20 C +ATOM 101 C LEU A 16 26.614 -1.169 16.344 1.00 20.28 C +ATOM 102 O LEU A 16 25.599 -0.734 16.933 1.00 18.32 O +ATOM 103 CB LEU A 16 27.811 -3.027 17.542 1.00 19.70 C +ATOM 104 CG LEU A 16 27.384 -2.550 18.921 1.00 22.23 C +ATOM 105 CD1 LEU A 16 26.031 -3.234 19.257 1.00 27.80 C +ATOM 106 CD2 LEU A 16 28.445 -2.970 19.933 1.00 21.91 C +ATOM 107 N ILE A 17 27.514 -0.365 15.791 1.00 20.97 N +ATOM 108 CA ILE A 17 27.343 1.056 15.618 1.00 20.41 C +ATOM 109 C ILE A 17 26.081 1.392 14.758 1.00 18.17 C +ATOM 110 O ILE A 17 25.380 2.240 15.282 1.00 16.46 O +ATOM 111 CB ILE A 17 28.579 1.847 15.132 1.00 21.10 C +ATOM 112 CG1 ILE A 17 29.586 1.858 16.352 1.00 25.66 C +ATOM 113 CG2 ILE A 17 28.268 3.288 14.691 1.00 22.04 C +ATOM 114 CD1 ILE A 17 30.856 2.696 16.161 1.00 27.00 C +ATOM 115 N SER A 18 25.930 0.759 13.657 1.00 16.97 N +ATOM 116 CA SER A 18 24.825 0.827 12.744 1.00 19.98 C +ATOM 117 C SER A 18 23.499 0.405 13.438 1.00 18.89 C +ATOM 118 O SER A 18 22.557 1.165 13.352 1.00 18.37 O +ATOM 119 CB SER A 18 25.076 0.039 11.491 1.00 20.39 C +ATOM 120 OG SER A 18 23.902 0.046 10.670 1.00 23.87 O +ATOM 121 N TRP A 19 23.512 -0.661 14.161 1.00 17.71 N +ATOM 122 CA TRP A 19 22.492 -1.085 15.081 1.00 15.72 C +ATOM 123 C TRP A 19 22.083 0.004 16.012 1.00 18.02 C +ATOM 124 O TRP A 19 20.820 0.244 16.160 1.00 16.93 O +ATOM 125 CB TRP A 19 22.854 -2.410 15.767 1.00 15.59 C +ATOM 126 CG TRP A 19 21.803 -2.993 16.678 1.00 17.94 C +ATOM 127 CD1 TRP A 19 20.917 -3.950 16.210 1.00 18.03 C +ATOM 128 CD2 TRP A 19 21.448 -2.745 18.041 1.00 16.03 C +ATOM 129 NE1 TRP A 19 20.060 -4.304 17.222 1.00 21.28 N +ATOM 130 CE2 TRP A 19 20.357 -3.624 18.372 1.00 20.45 C +ATOM 131 CE3 TRP A 19 21.879 -1.892 19.048 1.00 14.41 C +ATOM 132 CZ2 TRP A 19 19.784 -3.690 19.612 1.00 17.15 C +ATOM 133 CZ3 TRP A 19 21.292 -1.950 20.288 1.00 17.24 C +ATOM 134 CH2 TRP A 19 20.230 -2.805 20.601 1.00 15.13 C +ATOM 135 N ILE A 20 22.930 0.594 16.823 1.00 14.82 N +ATOM 136 CA ILE A 20 22.628 1.633 17.766 1.00 15.67 C +ATOM 137 C ILE A 20 21.917 2.819 17.080 1.00 17.51 C +ATOM 138 O ILE A 20 20.942 3.365 17.655 1.00 17.70 O +ATOM 139 CB ILE A 20 23.902 2.192 18.499 1.00 16.25 C +ATOM 140 CG1 ILE A 20 24.481 0.986 19.363 1.00 15.50 C +ATOM 141 CG2 ILE A 20 23.599 3.421 19.390 1.00 14.54 C +ATOM 142 CD1 ILE A 20 26.033 1.304 19.637 1.00 18.18 C +ATOM 143 N LYS A 21 22.464 3.177 15.957 1.00 16.61 N +ATOM 144 CA LYS A 21 21.888 4.236 15.157 1.00 19.84 C +ATOM 145 C LYS A 21 20.436 3.910 14.752 1.00 21.02 C +ATOM 146 O LYS A 21 19.685 4.899 14.971 1.00 22.80 O +ATOM 147 CB LYS A 21 22.699 4.646 13.935 1.00 16.73 C +ATOM 148 CG LYS A 21 23.944 5.416 14.471 1.00 22.19 C +ATOM 149 CD LYS A 21 24.919 5.669 13.300 1.00 25.86 C +ATOM 150 CE LYS A 21 26.173 6.287 13.908 1.00 32.91 C +ATOM 151 NZ LYS A 21 27.199 6.564 12.863 1.00 39.11 N +ATOM 152 N ARG A 22 20.075 2.728 14.351 1.00 19.18 N +ATOM 153 CA ARG A 22 18.740 2.273 14.020 1.00 20.38 C +ATOM 154 C ARG A 22 17.807 2.365 15.177 1.00 22.46 C +ATOM 155 O ARG A 22 16.648 2.899 15.096 1.00 23.24 O +ATOM 156 CB ARG A 22 18.733 0.860 13.418 1.00 22.73 C +ATOM 157 CG ARG A 22 19.309 0.956 12.004 1.00 22.29 C +ATOM 158 CD ARG A 22 19.117 -0.300 11.254 1.00 25.78 C +ATOM 159 NE ARG A 22 19.382 -1.562 11.991 1.00 28.94 N +ATOM 160 CZ ARG A 22 20.624 -2.104 11.889 1.00 33.77 C +ATOM 161 NH1 ARG A 22 21.664 -1.554 11.252 1.00 31.21 N +ATOM 162 NH2 ARG A 22 20.870 -3.271 12.498 1.00 33.11 N +END diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2/para_HB b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2/para_HB new file mode 100644 index 00000000..df4195dc --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2/para_HB @@ -0,0 +1,41 @@ + 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 0.00000 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b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2/single_frags.mem new file mode 100644 index 00000000..df1a9830 --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2/single_frags.mem @@ -0,0 +1,5 @@ +[Target] +query + +[Memories] +2mlt_frag2_A.gro 1 14 9 20 diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2/ssweight b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2/ssweight new file mode 100644 index 00000000..1a511e32 --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2/ssweight @@ -0,0 +1,9 @@ +1.0 0.0 +1.0 0.0 +1.0 0.0 +1.0 0.0 +1.0 0.0 +1.0 0.0 +1.0 0.0 +1.0 0.0 +0.0 0.0 diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2/ssweight.stride b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2/ssweight.stride new file mode 100644 index 00000000..161e4900 --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/2mlt_frag2/ssweight.stride @@ -0,0 +1,24 @@ +REM -------------------- Secondary structure summary ------------------- ~~~~ +REM ~~~~ +CHN crystal_structure.pdb A ~~~~ +REM ~~~~ +REM ~~~~ +SEQ 1 PALISWIKR 9 ~~~~ +STR HHHHHHHH ~~~~ +REM ~~~~ +REM ~~~~ +REM ~~~~ +LOC AlphaHelix PRO 14 A LYS 21 A ~~~~ +REM ~~~~ +REM --------------- Detailed secondary structure assignment------------- ~~~~ +REM ~~~~ +REM |---Residue---| |--Structure--| |-Phi-| |-Psi-| |-Area-| ~~~~ +ASG PRO A 14 1 H AlphaHelix 360.00 -46.34 148.7 ~~~~ +ASG ALA A 15 2 H AlphaHelix -67.75 -40.73 82.0 ~~~~ +ASG LEU A 16 3 H AlphaHelix -57.70 -40.75 119.2 ~~~~ +ASG ILE A 17 4 H AlphaHelix -58.49 -48.66 97.6 ~~~~ +ASG SER A 18 5 H AlphaHelix -59.75 -46.13 55.6 ~~~~ +ASG TRP A 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b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/lammps_movie.pdb new file mode 100644 index 00000000..b3e12d78 --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/lammps_movie.pdb @@ -0,0 +1,53 @@ +MODEL 1 +ATOM 1 CA PRO A 1 31.026 -1.278 13.03 1.00 0.00 C +ATOM 2 C PRO A 1 29.512 -1.628 12.866 1.00 0.00 C +ATOM 3 O PRO A 1 28.657 -0.801 12.744 1.00 0.00 O +ATOM 4 CB PRO A 1 31.845 -1.614 11.816 1.00 0.00 C +ATOM 5 N ALA A 2 29.215 -2.872 12.869 1.00 0.00 N +ATOM 6 H ALA A 2 29.906 -3.539 12.968 1.00 0.00 H +ATOM 7 CA ALA A 2 27.822 -3.418 12.724 1.00 0.00 C +ATOM 8 C ALA A 2 26.993 -2.959 13.913 1.00 0.00 C +ATOM 9 O ALA A 2 25.872 -2.551 13.769 1.00 0.00 O +ATOM 10 CB ALA A 2 27.741 -4.906 12.502 1.00 0.00 C +ATOM 11 N LEU A 3 27.579 -3.039 15.08 1.00 0.00 N +ATOM 12 H LEU A 3 28.484 -3.368 15.197 1.00 0.00 H +ATOM 13 CA LEU A 3 26.958 -2.649 16.351 1.00 0.00 C +ATOM 14 C LEU A 3 26.612 -1.163 16.366 1.00 0.00 C +ATOM 15 O LEU A 3 25.599 -0.734 16.933 1.00 0.00 O +ATOM 16 CB LEU A 3 27.811 -3.027 17.542 1.00 0.00 C +ATOM 17 N ILE A 4 27.483 -0.4 15.728 1.00 0.00 N +ATOM 18 H ILE A 4 28.301 -0.746 15.27 1.00 0.00 H +ATOM 19 CA ILE A 4 27.343 1.056 15.618 1.00 0.00 C +ATOM 20 C ILE A 4 26.12 1.382 14.834 1.00 0.00 C +ATOM 21 O ILE A 4 25.38 2.24 15.282 1.00 0.00 O +ATOM 22 CB ILE A 4 28.579 1.847 15.132 1.00 0.00 C +ATOM 23 N SER A 5 25.939 0.674 13.66 1.00 0.00 N +ATOM 24 H SER A 5 26.537 -0.017 13.299 1.00 0.00 H +ATOM 25 CA SER A 5 24.825 0.827 12.744 1.00 0.00 C +ATOM 26 C SER A 5 23.548 0.486 13.489 1.00 0.00 C +ATOM 27 O SER A 5 22.557 1.165 13.352 1.00 0.00 O +ATOM 28 CB SER A 5 25.076 0.039 11.491 1.00 0.00 C +ATOM 29 N TRP A 6 23.608 -0.581 14.275 1.00 0.00 N +ATOM 30 H TRP A 6 24.408 -1.128 14.386 1.00 0.00 H +ATOM 31 CA TRP A 6 22.492 -1.085 15.081 1.00 0.00 C +ATOM 32 C TRP A 6 21.987 -0.019 16.059 1.00 0.00 C +ATOM 33 O TRP A 6 20.82 0.244 16.16 1.00 0.00 O +ATOM 34 CB TRP A 6 22.854 -2.41 15.767 1.00 0.00 C +ATOM 35 N ILE A 7 22.9 0.579 16.769 1.00 0.00 N +ATOM 36 H ILE A 7 23.842 0.367 16.688 1.00 0.00 H +ATOM 37 CA ILE A 7 22.628 1.633 17.766 1.00 0.00 C +ATOM 38 C ILE A 7 21.913 2.801 17.117 1.00 0.00 C +ATOM 39 O ILE A 7 20.942 3.365 17.655 1.00 0.00 O +ATOM 40 CB ILE A 7 23.902 2.192 18.499 1.00 0.00 C +ATOM 41 N LYS A 8 22.423 3.141 15.952 1.00 0.00 N +ATOM 42 H LYS A 8 23.206 2.686 15.519 1.00 0.00 H +ATOM 43 CA LYS A 8 21.888 4.236 15.157 1.00 0.00 C +ATOM 44 C LYS A 8 20.44 3.987 14.83 1.00 0.00 C +ATOM 45 O LYS A 8 19.685 4.899 14.971 1.00 0.00 O +ATOM 46 CB LYS A 8 22.699 4.646 13.935 1.00 0.00 C +ATOM 47 N ARG A 9 20.086 2.732 14.393 1.00 0.00 N +ATOM 48 H ARG A 9 20.695 1.997 14.279 1.00 0.00 H +ATOM 49 CA ARG A 9 18.74 2.273 14.02 1.00 0.00 C +ATOM 50 O ARG A 9 16.648 2.899 15.096 1.00 0.00 O +ATOM 51 CB ARG A 9 18.733 0.86 13.418 1.00 0.00 C +ENDMDL diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/lammps_movie.psf b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/lammps_movie.psf new file mode 100644 index 00000000..5140a19a --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/lammps_movie.psf @@ -0,0 +1,69 @@ +PSF + + 0 !NTITLE + + 51 !NATOM + 1 PROT 1 PRO CA C 0 1 0 + 2 PROT 1 PRO C C 0 1 0 + 3 PROT 1 PRO O O 0 1 0 + 4 PROT 1 PRO CB C 0 1 0 + 5 PROT 2 ALA N N 0 1 0 + 6 PROT 2 ALA H H 0 1 0 + 7 PROT 2 ALA CA C 0 1 0 + 8 PROT 2 ALA C C 0 1 0 + 9 PROT 2 ALA O O 0 1 0 + 10 PROT 2 ALA CB C 0 1 0 + 11 PROT 3 LEU N N 0 1 0 + 12 PROT 3 LEU H H 0 1 0 + 13 PROT 3 LEU CA C 0 1 0 + 14 PROT 3 LEU C C 0 1 0 + 15 PROT 3 LEU O O 0 1 0 + 16 PROT 3 LEU CB C 0 1 0 + 17 PROT 4 ILE N N 0 1 0 + 18 PROT 4 ILE H H 0 1 0 + 19 PROT 4 ILE CA C 0 1 0 + 20 PROT 4 ILE C C 0 1 0 + 21 PROT 4 ILE O O 0 1 0 + 22 PROT 4 ILE CB C 0 1 0 + 23 PROT 5 SER 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47 49 + 49 51 \ No newline at end of file diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/lammps_stdout.txt b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/lammps_stdout.txt new file mode 100644 index 00000000..db9c7529 --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/lammps_stdout.txt @@ -0,0 +1,227 @@ +LAMMPS (29 Aug 2024 - Update 1) +Reading data file ... + orthogonal box = (-200 -200 -200) to (200 200 200) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 27 atoms + scanning bonds ... + 3 = max bonds/atom + orthogonal box = (-200.04 -200.04 -200.04) to (200.04 200.04 200.04) + 1 by 1 by 1 MPI processor grid + reading bonds ... + 34 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 1 1 + 5 = max # of 1-2 neighbors + 5 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.011 seconds +9 atoms in group alpha_carbons +9 atoms in group beta_atoms +9 atoms in group oxygens +Chain flag on +Chi flag on +Rama flag on +Rama_P flag on +SSWeight flag on +ABC flag on +Dssp_Hdrgn flag on +P_AP flag on +Water flag on +Burial flag on +Helix flag on + +Fix backbone Pair List cutoff 15.0000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: +- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419 +The log file lists these citations in BibTeX format. + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Generated 0 of 10 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 5 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14.5 + ghost atom cutoff = 25 + binsize = 7.25, bins = 3 2 1 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair vexcluded, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) fix backbone, perpetual + attributes: half, newton on, cut 25 + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:1202) +Setting up Verlet run ... + Unit style : real + Current step : 0 + Time step : 2 +theta: 0.000119074 +theta: 0.999944 +theta: 0.00128363 +theta: 1.45934e-05 +theta: 0.999985 +theta: 0.832683 +theta: 1.12339e-05 +theta: 0.999987 +theta: 0.21988 +theta: 9.37758e-05 +theta: 0.999962 +theta: 0.154699 +theta: 2.38715e-06 +theta: 0.999979 +theta: 0.0745674 +theta: 1.53811e-05 +theta: 0.999968 +theta: 5.16896e-06 +ires: 0 + helix_par.kappa_sigma: 7 + helix_par.treshold: 3 + helix_ro[ires]: 1.00135 +ires: 1 + helix_par.kappa_sigma: 7 + helix_par.treshold: 3 + helix_ro[ires]: 1.83268 +ires: 2 + helix_par.kappa_sigma: 7 + helix_par.treshold: 3 + helix_ro[ires]: 1.22 +ires: 3 + helix_par.kappa_sigma: 7 + helix_par.treshold: 3 + helix_ro[ires]: 2.15471 +ires: 4 + helix_par.kappa_sigma: 7 + helix_par.treshold: 3 + helix_ro[ires]: 2.07583 +ires: 5 + helix_par.kappa_sigma: 7 + helix_par.treshold: 3 + helix_ro[ires]: 2.83275 +ires: 6 + helix_par.kappa_sigma: 7 + helix_par.treshold: 3 + helix_ro[ires]: 1.21985 +ires: 7 + helix_par.kappa_sigma: 7 + helix_par.treshold: 3 + helix_ro[ires]: 1.15469 +ires: 8 + helix_par.kappa_sigma: 7 + helix_par.treshold: 3 + helix_ro[ires]: 1.07454 +se[j_resno]: S +xn[j]: 25.9391 0.674258 13.66 +xh[j]: 26.5371 -0.0173397 13.2993 +dr_NO: 0.239083 +dr_HO: 0.17156 +dr_NO_sigma: 0.517047 +dr_HO_sigma: 0.297022 +R_NO: 3.22528 +helix_NO_zero: 2.9862 +R_HO: 2.32736 +helix_HO_zero: 2.1558 +helix_sigma_h[i_resno]: 1 +helix_sigma_h[j_resno]: 0.999998 +helix_gamma_p: 2 +helix_gamma_w: -1 +se[j_resno]: W +xn[j]: 23.608 -0.580657 14.2747 +xh[j]: 24.4079 -1.12834 14.3855 +dr_NO: 0.0574551 +dr_HO: -0.0232902 +dr_NO_sigma: 0.124254 +dr_HO_sigma: -0.0403223 +R_NO: 3.04366 +helix_NO_zero: 2.9862 +R_HO: 2.13251 +helix_HO_zero: 2.1558 +helix_sigma_h[i_resno]: 1 +helix_sigma_h[j_resno]: 0.912261 +helix_gamma_p: 2 +helix_gamma_w: -1 +se[j_resno]: I +xn[j]: 22.9002 0.578721 16.7687 +xh[j]: 23.8421 0.36665 16.6878 +dr_NO: 0.0194471 +dr_HO: -0.0681403 +dr_NO_sigma: 0.042057 +dr_HO_sigma: -0.117971 +R_NO: 3.00565 +helix_NO_zero: 2.9862 +R_HO: 2.08766 +helix_HO_zero: 2.1558 +helix_sigma_h[i_resno]: 1 +helix_sigma_h[j_resno]: 1 +helix_gamma_p: 2 +helix_gamma_w: -1 +se[j_resno]: K +xn[j]: 22.4227 3.14081 15.9525 +xh[j]: 23.2061 2.68639 15.519 +dr_NO: 0.177115 +dr_HO: 0.0760412 +dr_NO_sigma: 0.383034 +dr_HO_sigma: 0.13165 +R_NO: 3.16331 +helix_NO_zero: 2.9862 +R_HO: 2.23184 +helix_HO_zero: 2.1558 +helix_sigma_h[i_resno]: 0.999993 +helix_sigma_h[j_resno]: 1 +helix_gamma_p: 2 +helix_gamma_w: -1 +se[j_resno]: R +xn[j]: 20.0856 2.73201 14.3926 +xh[j]: 20.6953 1.99685 14.2793 +dr_NO: 0.11966 +dr_HO: 0.084265 +dr_NO_sigma: 0.258779 +dr_HO_sigma: 0.145888 +R_NO: 3.10586 +helix_NO_zero: 2.9862 +R_HO: 2.24006 +helix_HO_zero: 2.1558 +helix_sigma_h[i_resno]: 0.999998 +helix_sigma_h[j_resno]: 1 +helix_gamma_p: 2 +helix_gamma_w: -1 +Per MPI rank memory allocation (min/avg/max) = 7.185 | 7.185 | 7.185 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 0 300 0.88896901 204.53961 228.6789 -71774.674 1070.3864 +Loop time of 7.37e-07 on 1 procs for 0 steps with 27 atoms + +135.7% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Bond | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 7.37e-07 | | |100.00 + +Nlocal: 27 ave 27 max 27 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 313 ave 313 max 313 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 313 +Ave neighs/atom = 11.592593 +Ave special neighs/atom = 2.5185185 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/log.lammps b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/log.lammps new file mode 100644 index 00000000..5fe9c0f1 --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/log.lammps @@ -0,0 +1,156 @@ +LAMMPS (29 Aug 2024 - Update 1) +# 3d protein simulation + +units real + +timestep 2 + +dimension 3 + +boundary s s s +#boundary p p p + +neighbor 10 bin +neigh_modify delay 5 + +atom_modify sort 0 0.0 + +special_bonds fene + +atom_style awsemmd + +bond_style harmonic + +pair_style vexcluded 2 3.5 3.5 + +read_data data.2mlt_frag2 +Reading data file ... + orthogonal box = (-200 -200 -200) to (200 200 200) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 27 atoms + scanning bonds ... + 3 = max bonds/atom + orthogonal box = (-200.04 -200.04 -200.04) to (200.04 200.04 200.04) + 1 by 1 by 1 MPI processor grid + reading bonds ... + 34 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 1 1 + 5 = max # of 1-2 neighbors + 5 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.011 seconds + +pair_coeff * * 0.0 +pair_coeff 1 1 20.0 3.5 4.5 +pair_coeff 1 4 20.0 3.5 4.5 +pair_coeff 4 4 20.0 3.5 4.5 +pair_coeff 3 3 20.0 3.5 3.5 + + +velocity all create 300.0 2349852 + +group alpha_carbons id 1 4 7 10 13 16 19 22 25 +9 atoms in group alpha_carbons + +group beta_atoms id 3 6 9 12 15 18 21 24 27 +9 atoms in group beta_atoms + +group oxygens id 2 5 8 11 14 17 20 23 26 +9 atoms in group oxygens + + +fix 1 all nvt temp 300.0 300.0 100.0 +fix 2 alpha_carbons backbone beta_atoms oxygens fix_backbone_coeff.data 2mlt_frag2.seq +Chain flag on +Chi flag on +Rama flag on +Rama_P flag on +SSWeight flag on +ABC flag on +Dssp_Hdrgn flag on +P_AP flag on +Water flag on +Burial flag on +Helix flag on + +Fix backbone Pair List cutoff 15.0000 + +thermo 1000 +dump 1 all atom 1000 dump.lammpstrj + +dump_modify 1 sort id + +reset_timestep 0 +run 0 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419 + +@Article{Gissinger24, + author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor}, + title = {Type Label Framework for Bonded Force Fields in LAMMPS}, + journal = {J. Phys. Chem. B}, + year = 2024, + volume = 128, + number = 13, + pages = {3282–-3297} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Generated 0 of 10 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 5 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14.5 + ghost atom cutoff = 25 + binsize = 7.25, bins = 3 2 1 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair vexcluded, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + (2) fix backbone, perpetual + attributes: half, newton on, cut 25 + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:1202) +Per MPI rank memory allocation (min/avg/max) = 7.185 | 7.185 | 7.185 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 0 300 0.88896901 204.53961 228.6789 -71774.674 1070.3864 +Loop time of 7.37e-07 on 1 procs for 0 steps with 27 atoms + +135.7% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Bond | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 7.37e-07 | | |100.00 + +Nlocal: 27 ave 27 max 27 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 313 ave 313 max 313 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 313 +Ave neighs/atom = 11.592593 +Ave special neighs/atom = 2.5185185 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/para_HB 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0.00000 0.00000 1.99465 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.79318 1.21189 0.00000 0.00000 -0.63993 + 0.00000 1.20939 0.00000 0.00000 1.03964 0.00000 0.00000 0.00000 1.53789 0.00000 -1.78384 0.00000 0.00000 0.00000 1.42011 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 1.60720 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 0.00000 1.17581 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.80971 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00000 0.00000 -1.85438 -1.17893 0.00000 0.00000 0.00000 -0.74379 0.00000 0.00000 0.00000 -1.70023 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 -0.59377 0.18153 diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/para_one b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/para_one new file mode 100644 index 00000000..9547ca68 --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/para_one @@ -0,0 +1,20 @@ + 4.59413901E-2 + -1.14228296 + -0.980181694 + -0.954810441 + 6.045979261E-2 + -0.940543473 + -0.944277942 + -0.326405674 + -0.517350674 + 0.674874783 + 0.559263945 + -1.37892628 + 0.311426193 + 0.229282543 + -0.544425964 + -0.59238559 + -0.701828241 + -0.337591201 + -0.414966911 + 0.660636663 diff --git a/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/ssweight b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/ssweight new file mode 100644 index 00000000..1a511e32 --- /dev/null +++ b/tests/data/test_implementation_of_lammps_hbond_energies/make_test_for_2mlt_frag2/ssweight @@ -0,0 +1,9 @@ +1.0 0.0 +1.0 0.0 +1.0 0.0 +1.0 0.0 +1.0 0.0 +1.0 0.0 +1.0 0.0 +1.0 0.0 +0.0 0.0 diff --git a/tests/test_energies.py b/tests/test_energies.py index 56604db6..cfd4ec51 100644 --- a/tests/test_energies.py +++ b/tests/test_energies.py @@ -56,7 +56,16 @@ def time_many(func): def set_up_forces(oa, protein, force_name=None): #Define all forces using lambda to delay execution of the setup. all_forces = { - "Backbone": lambda: openawsem.functionTerms.basicTerms.con_term(oa), + # Usually, the backbone is considered to include chain, chi, and excl in addition to con. + # Sometimes, it is also considered to include the various Rama terms. + # + # Even though the "Backbone" key defined here includes only the con term, + # the default force_name=None use of this function results in all of the + # following terms being added to the OpenMM System and, since Con, Chain, + # Chi, and Excluded all use forceGroup 20, the Con+Chi+Chain+Excluded sum + # will be returned when any one of the 4 terms is queried. + # + "Backbone": lambda: openawsem.functionTerms.basicTerms.con_term(oa), "Rama": lambda: openawsem.functionTerms.basicTerms.rama_term(oa), "Contact": lambda: openawsem.functionTerms.contactTerms.contact_term(oa), "Chain": lambda: openawsem.functionTerms.basicTerms.chain_term(oa), @@ -105,6 +114,8 @@ def analyze(protein, simulation_platform): integrator = openmm.LangevinIntegrator(300*openawsem.unit_definitions.kelvin, 1/openawsem.unit_definitions.picosecond, 2*openawsem.unit_definitions.femtoseconds) simulation = openmm.app.Simulation(oa.pdb.topology, oa.system, integrator, platform) + # "Backbone" test returns the Con+Chi+Chain+Excluded sum, since set_up_forces was called with force_name=None + # (see the note in the set_up_forces function defined at the beginning of his file) forceGroupTable = {"Backbone": 20, "Rama": 21, "Contact": 22, "Fragment": 23, "Membrane": 24, "ER": 25, "TBM_Q": 26, "Beta": 27, "Pap": 28, "Helical": 29, "Q": 1, "Rg": 2, "Qc": 3, "Helix_orientation": 18, "Pulling": 19} diff --git a/tests/test_implementation_of_lammps_hbond_energies_alpha.py b/tests/test_implementation_of_lammps_hbond_energies_alpha.py new file mode 100644 index 00000000..0e0d5cc7 --- /dev/null +++ b/tests/test_implementation_of_lammps_hbond_energies_alpha.py @@ -0,0 +1,162 @@ +#!/usr/bin/env python3 +import pandas as pd +import mdtraj as md +import numpy as np +import time +import openmm +import openawsem +import pytest +import functools +from pathlib import Path + +""" +compares OpenAWSEM implementation of alpha helical hbond energy from LAMMPS AWSEM-MD commit cea754f +(https://github.com/adavtyan/awsemmd/tree/cea754f1208fde6332d4d0f1cae3212bf7e8afbb) to energies computed by the LAMMPS code +""" + + +PROTEINS = ["2mlt_1to5","2mlt_frag1","2mlt_frag2",]#"2mlt_full"] # 2mlt_full too big, leading to super slow energy evaluation i guess + #(the number of terms in the energy string are O(N^2) where N is the number of residues) +COLUMNS = ["Beta","Pap","Helical"] +# we include the Beta and P-AP columns, but they aren't expected to be interesting for these structures +# or meaningfully test the implementation of those terms +PLATFORMS = ['Reference', 'CPU', 'CUDA'] # ["OpenCL"] # even these smaller systems were eating RAM on OpenCL on my desktop +data_path = Path('tests')/'data'/'test_implementation_of_lammps_hbond_energies' + + +def single_run(func): + @functools.wraps(func) + def wrapper(*args, **kwargs): + start_time = time.time() + result = func(*args, **kwargs) + end_time = time.time() + elapsed_time = end_time - start_time + return result, elapsed_time*1000 + return wrapper + +def repeated_run(func): + @functools.wraps(func) + def wrapper(*args, **kwargs): + total_time = 0 + executions = 0 + # Run the function repeatedly until the total time is at least 10 seconds + while total_time < 20: + start_time = time.time() + result = func(*args, **kwargs) + end_time = time.time() + elapsed_time = end_time - start_time + total_time += elapsed_time + executions += 1 + # Calculate average time (in milliseconds) per execution + average_time = (total_time / executions) * 1000 + return result, average_time + return wrapper + + +@single_run +def time_once(func): + return func() + +@repeated_run +def time_many(func): + return func() + + +def set_up_forces(oa, protein, force_name=None): + #Define all forces using lambda to delay execution of the setup. + all_forces = { + "RamaSSWeight": lambda: openawsem.functionTerms.basicTerms.rama_ssweight_term(oa, k_rama_ssweight=2*8.368, ssweight_file=data_path/f'{protein}-ssweight'), + "Beta1": lambda: openawsem.functionTerms.hydrogenBondTerms.beta_term_1_old(oa,k_beta=0.5*4.184,ssweight_file=data_path/f'{protein}-ssweight'), + "Beta2": lambda: openawsem.functionTerms.hydrogenBondTerms.beta_term_2_old(oa,k_beta=0.5*4.184,ssweight_file=data_path/f'{protein}-ssweight'), + "Beta3": lambda: openawsem.functionTerms.hydrogenBondTerms.beta_term_3_old(oa,k_beta=0.5*4.184,ssweight_file=data_path/f'{protein}-ssweight'), + "Helical": lambda: openawsem.functionTerms.hydrogenBondTerms.density_dependent_helical_term(oa,k_helical=0.5*4.184,forceGroup=29), + "Pap": lambda: openawsem.functionTerms.hydrogenBondTerms.pap_term_old(oa,k_pap=0.5*4.184,ssweight_file=data_path/f'{protein}-ssweight',forceGroup=28), + } + + forces = [] + if force_name: + if force_name not in all_forces: + raise ValueError(f"Force {force_name} is not recognized.") + force = all_forces[force_name]() + forces.append(force) + else: + for force_name, force_func in all_forces.items(): + force = force_func() + forces.append(force) + + return forces + +def analyze(protein, simulation_platform): + chain = openawsem.helperFunctions.myFunctions.getAllChains(data_path/f"{protein}-crystal_structure.pdb") + seq = openawsem.helperFunctions.myFunctions.read_fasta(data_path/f"{protein}-crystal_structure.fasta") + pdb_trajectory = md.load(data_path/f'{protein}-movie.dcd', top=data_path/f"{protein}-openmmawsem.pdb") + + oa = openawsem.OpenMMAWSEMSystem(data_path/f"{protein}-openmmawsem.pdb", + chains=chain, + k_awsem=1.0, + xml_filename=openawsem.xml, + seqFromPdb=seq, + includeLigands=False) + + forces = set_up_forces(oa, protein) + oa.addForcesWithDefaultForceGroup(forces) + + platform = openmm.Platform.getPlatformByName(simulation_platform) + integrator = openmm.LangevinIntegrator(300*openawsem.unit_definitions.kelvin, 1/openawsem.unit_definitions.picosecond, 2*openawsem.unit_definitions.femtoseconds) + simulation = openmm.app.Simulation(oa.pdb.topology, oa.system, integrator, platform) + + forceGroupTable = {"Beta": {23,24,25}, "Pap": {28}, "Helical": {29},} + + termEnergies = pd.DataFrame(columns=["Step"] + COLUMNS) + + for step in range(len(pdb_trajectory)): + simulation.context.setPositions(pdb_trajectory.openmm_positions(step)) + e = [] + for term in COLUMNS: + g = forceGroupTable[term] + state = simulation.context.getState(getEnergy=True, groups=g) + # note that we use kcal/mol instead of kJ/mol because we're comparing to lammps, which uses kcal/mol + termEnergy = state.getPotentialEnergy().value_in_unit(openawsem.unit_definitions.kilocalories_per_mole) + e.append(termEnergy) + termEnergies.loc[step] = [step] + e + + return termEnergies + + +# Cache to store analyzed data +analyzed_data_cache = {} + +@pytest.fixture(scope="session") +def analyzed_data(): + def get_data(protein, simulation_platform): + # Create a unique key for each protein and platform combination + key = (protein, simulation_platform) + + # If the data has already been computed, return it from the cache + if key in analyzed_data_cache: + return analyzed_data_cache[key] + + # Otherwise, compute the data and store it in the cache + analyzed_data_cache[key] = analyze(protein, simulation_platform) + return analyzed_data_cache[key] + + # Return the function that accesses data, either from cache or by computing + return get_data + +@pytest.mark.parametrize("column", COLUMNS) +@pytest.mark.parametrize("platform", PLATFORMS) +class TestEnergyTerms: + def test_energy_term(self, platform, column, analyzed_data): + tolerance = 1e-4 # note the higher tolerance than the 1e-5 used in test_energies.py + for protein in PROTEINS: + calculated_energies = analyzed_data(protein, platform) + saved_energies = pd.read_csv(data_path/f'{protein}_energies.csv') + + assert column in calculated_energies.columns, f"Column {column} not found in calculated energies for protein {protein} on platform {platform}" + assert column in saved_energies.columns, f"Column {column} not found in saved energies for protein {protein} on platform {platform},-----{saved_energies.columns}" + assert np.allclose(calculated_energies[column], saved_energies[column], atol=tolerance), f"Energy terms comparison failed for protein {protein} on column {column} on platform {platform}" + + +if __name__ == '__main__': + # not executed by pytest + pass