Parametrizing Co-factors for FESetup

[ecdybeck]

Hello,

I would like to run a simulation of a ligand binding to a protein with a co-factor. I see in an earlier post (December 14-16) it was stated that one could run with a co-factor by including it with the protein. Could you be more specific on exactly how one includes the co-factor in the set-up process?

Right now, I am getting an error from tleap, which I have copied below. I think this is because it is looking to assign protein parameters to the small molecule co-factor? Do I have to pre-parametrize the co-factor and then add it in as a user parameter file? Do I have to split the pdb file into one of the protein and one of the co-factor and then combine them later? Thanks in advance for your help. I can attach the .in file or other files I am using upon request.

FATAL: Atom .R<3M3 461>.A<FAC 18> does not have a type.
FATAL: Atom .R<3M3 461>.A<OAM 17> does not have a type.
FATAL: Atom .R<3M3 461>.A<NAL 16> does not have a type.
FATAL: Atom .R<3M3 461>.A<NAK 15> does not have a type.
FATAL: Atom .R<3M3 461>.A<CAR 14> does not have a type.
FATAL: Atom .R<3M3 461>.A<CAQ 13> does not have a type.
FATAL: Atom .R<3M3 461>.A<CAP 12> does not have a type.
FATAL: Atom .R<3M3 461>.A<CAO 11> does not have a type.
FATAL: Atom .R<3M3 461>.A<CAN 10> does not have a type.
FATAL: Atom .R<3M3 461>.A<CAJ 9> does not have a type.
FATAL: Atom .R<3M3 461>.A<CAI 8> does not have a type.
FATAL: Atom .R<3M3 461>.A<CAH 7> does not have a type.
FATAL: Atom .R<3M3 461>.A<CAG 6> does not have a type.
FATAL: Atom .R<3M3 461>.A<CAF 5> does not have a type.
FATAL: Atom .R<3M3 461>.A<CAE 4> does not have a type.
FATAL: Atom .R<3M3 461>.A<CAD 3> does not have a type.
FATAL: Atom .R<3M3 461>.A<CAB 2> does not have a type.
FATAL: Atom .R<3M3 461>.A<CAA 1> does not have a type.

[skfegan]

Hi,

You would need to parameterize the co-factor yourself. The cofactor.frcmod and cofactor.prep files should be in the directory from which you are running FESetup and you will need to use the 'user_params = True' in the [globals] section of your .in file. The cofactor should be in the same pdb file as the protein.

You might need to replace the FESetup/lib/python2.7/site-packages/FESetup directory in the FESetup source code with the dev version to get the user_params option to work.