diff --git a/data_paper_examples/ethylamine_dendrimer.itp b/data_paper_examples/ethylamine_dendrimer.itp index 587761c..1865814 100644 --- a/data_paper_examples/ethylamine_dendrimer.itp +++ b/data_paper_examples/ethylamine_dendrimer.itp @@ -95,55 +95,55 @@ 27 HC 4 BB6C H11 27 0.060280 1.0080 28 HC 4 BB6C H12 28 0.060280 1.0080 29 NTer 4 BB6C N1 29 -0.590720 14.0067 - 30 CPos 5 BB6C C6 30 -0.137175 12.0110 - 31 HC 5 BB6C H13 31 0.116825 1.0080 - 32 HC 5 BB6C H14 32 0.116825 1.0080 - 33 CPos 5 BB6C C5 33 0.142825 12.0110 - 34 HC 5 BB6C H11 34 0.060825 1.0080 - 35 HC 5 BB6C H12 35 0.060825 1.0080 - 36 NTer 5 BB6C N1 36 -0.590175 14.0067 - 37 CPos 6 BB6C C6 37 -0.136771 12.0110 - 38 HC 6 BB6C H13 38 0.117229 1.0080 - 39 HC 6 BB6C H14 39 0.117229 1.0080 - 40 CPos 6 BB6C C5 40 0.143229 12.0110 - 41 HC 6 BB6C H11 41 0.061229 1.0080 - 42 HC 6 BB6C H12 42 0.061229 1.0080 - 43 NTer 6 BB6C N1 43 -0.589771 14.0067 - 44 CPos 7 BB6C C6 44 -0.136861 12.0110 - 45 HC 7 BB6C H13 45 0.117139 1.0080 - 46 HC 7 BB6C H14 46 0.117139 1.0080 - 47 CPos 7 BB6C C5 47 0.143139 12.0110 - 48 HC 7 BB6C H11 48 0.061139 1.0080 - 49 HC 7 BB6C H12 49 0.061139 1.0080 - 50 NTer 7 BB6C N1 50 -0.589861 14.0067 - 51 CPos 8 BB6C C6 51 -0.136721 12.0110 - 52 HC 8 BB6C H13 52 0.117279 1.0080 - 53 HC 8 BB6C H14 53 0.117279 1.0080 - 54 CPos 8 BB6C C5 54 0.143279 12.0110 - 55 HC 8 BB6C H11 55 0.061279 1.0080 - 56 HC 8 BB6C H12 56 0.061279 1.0080 - 57 NTer 8 BB6C N1 57 -0.589721 14.0067 - 58 CPos 9 BB6C C6 58 -0.136771 12.0110 - 59 HC 9 BB6C H13 59 0.117229 1.0080 - 60 HC 9 BB6C H14 60 0.117229 1.0080 - 61 CPos 9 BB6C C5 61 0.143229 12.0110 - 62 HC 9 BB6C H11 62 0.061229 1.0080 - 63 HC 9 BB6C H12 63 0.061229 1.0080 - 64 NTer 9 BB6C N1 64 -0.589771 14.0067 - 65 CPos 10 BB6C C6 65 -0.136861 12.0110 - 66 HC 10 BB6C H13 66 0.117139 1.0080 - 67 HC 10 BB6C H14 67 0.117139 1.0080 - 68 CPos 10 BB6C C5 68 0.143139 12.0110 - 69 HC 10 BB6C H11 69 0.061139 1.0080 - 70 HC 10 BB6C H12 70 0.061139 1.0080 - 71 NTer 10 BB6C N1 71 -0.589861 14.0067 - 72 CPos 11 BB6C C6 72 -0.136811 12.0110 - 73 HC 11 BB6C H13 73 0.117189 1.0080 - 74 HC 11 BB6C H14 74 0.117189 1.0080 - 75 CPos 11 BB6C C5 75 0.143189 12.0110 - 76 HC 11 BB6C H11 76 0.061189 1.0080 - 77 HC 11 BB6C H12 77 0.061189 1.0080 - 78 NTer 11 BB6C N1 78 -0.589811 14.0067 + 30 CPos 5 BB6C C6 30 -0.137266 12.0110 + 31 HC 5 BB6C H13 31 0.116734 1.0080 + 32 HC 5 BB6C H14 32 0.116734 1.0080 + 33 CPos 5 BB6C C5 33 0.142734 12.0110 + 34 HC 5 BB6C H11 34 0.060734 1.0080 + 35 HC 5 BB6C H12 35 0.060734 1.0080 + 36 NTer 5 BB6C N1 36 -0.590266 14.0067 + 37 CPos 6 BB6C C6 37 -0.136736 12.0110 + 38 HC 6 BB6C H13 38 0.117264 1.0080 + 39 HC 6 BB6C H14 39 0.117264 1.0080 + 40 CPos 6 BB6C C5 40 0.143264 12.0110 + 41 HC 6 BB6C H11 41 0.061264 1.0080 + 42 HC 6 BB6C H12 42 0.061264 1.0080 + 43 NTer 6 BB6C N1 43 -0.589736 14.0067 + 44 CPos 7 BB6C C6 44 -0.136786 12.0110 + 45 HC 7 BB6C H13 45 0.117214 1.0080 + 46 HC 7 BB6C H14 46 0.117214 1.0080 + 47 CPos 7 BB6C C5 47 0.143214 12.0110 + 48 HC 7 BB6C H11 48 0.061214 1.0080 + 49 HC 7 BB6C H12 49 0.061214 1.0080 + 50 NTer 7 BB6C N1 50 -0.589786 14.0067 + 51 CPos 8 BB6C C6 51 -0.136861 12.0110 + 52 HC 8 BB6C H13 52 0.117139 1.0080 + 53 HC 8 BB6C H14 53 0.117139 1.0080 + 54 CPos 8 BB6C C5 54 0.143139 12.0110 + 55 HC 8 BB6C H11 55 0.061139 1.0080 + 56 HC 8 BB6C H12 56 0.061139 1.0080 + 57 NTer 8 BB6C N1 57 -0.589861 14.0067 + 58 CPos 9 BB6C C6 58 -0.136736 12.0110 + 59 HC 9 BB6C H13 59 0.117264 1.0080 + 60 HC 9 BB6C H14 60 0.117264 1.0080 + 61 CPos 9 BB6C C5 61 0.143264 12.0110 + 62 HC 9 BB6C H11 62 0.061264 1.0080 + 63 HC 9 BB6C H12 63 0.061264 1.0080 + 64 NTer 9 BB6C N1 64 -0.589736 14.0067 + 65 CPos 10 BB6C C6 65 -0.136786 12.0110 + 66 HC 10 BB6C H13 66 0.117214 1.0080 + 67 HC 10 BB6C H14 67 0.117214 1.0080 + 68 CPos 10 BB6C C5 68 0.143214 12.0110 + 69 HC 10 BB6C H11 69 0.061214 1.0080 + 70 HC 10 BB6C H12 70 0.061214 1.0080 + 71 NTer 10 BB6C N1 71 -0.589786 14.0067 + 72 CPos 11 BB6C C6 72 -0.136861 12.0110 + 73 HC 11 BB6C H13 73 0.117139 1.0080 + 74 HC 11 BB6C H14 74 0.117139 1.0080 + 75 CPos 11 BB6C C5 75 0.143139 12.0110 + 76 HC 11 BB6C H11 76 0.061139 1.0080 + 77 HC 11 BB6C H12 77 0.061139 1.0080 + 78 NTer 11 BB6C N1 78 -0.589861 14.0067 79 CPos 12 BB6C C6 79 -0.136811 12.0110 80 HC 12 BB6C H13 80 0.117189 1.0080 81 HC 12 BB6C H14 81 0.117189 1.0080 @@ -151,660 +151,660 @@ 83 HC 12 BB6C H11 83 0.061189 1.0080 84 HC 12 BB6C H12 84 0.061189 1.0080 85 NTer 12 BB6C N1 85 -0.589811 14.0067 - 86 CPos 13 BB6C C6 86 -0.137442 12.0110 - 87 HC 13 BB6C H13 87 0.116558 1.0080 - 88 HC 13 BB6C H14 88 0.116558 1.0080 - 89 CPos 13 BB6C C5 89 0.142558 12.0110 - 90 HC 13 BB6C H11 90 0.060558 1.0080 - 91 HC 13 BB6C H12 91 0.060558 1.0080 - 92 NTer 13 BB6C N1 92 -0.590442 14.0067 - 93 HS14 14 PHGY H12 93 0.376830 1.0080 - 94 NPri 14 PHGY N2 94 -1.037170 14.0067 - 95 HS14 14 PHGY H11 95 0.376830 1.0080 - 96 CPos 14 PHGY C2 96 0.353830 12.0110 - 97 HC 14 PHGY H3 97 0.024830 1.0080 - 98 HC 14 PHGY H4 98 0.024830 1.0080 - 99 C 14 PHGY C1 99 -0.037170 12.0110 - 100 HC 14 PHGY H1 100 0.064830 1.0080 - 101 HC 14 PHGY H2 101 0.064830 1.0080 - 102 HS14 15 PHGY H12 102 0.377734 1.0080 - 103 NPri 15 PHGY N2 103 -1.036266 14.0067 - 104 HS14 15 PHGY H11 104 0.377734 1.0080 - 105 CPos 15 PHGY C2 105 0.354734 12.0110 - 106 HC 15 PHGY H3 106 0.025734 1.0080 - 107 HC 15 PHGY H4 107 0.025734 1.0080 - 108 C 15 PHGY C1 108 -0.036266 12.0110 - 109 HC 15 PHGY H1 109 0.065734 1.0080 - 110 HC 15 PHGY H2 110 0.065734 1.0080 - 111 HS14 16 PHGY H12 111 0.377699 1.0080 - 112 NPri 16 PHGY N2 112 -1.036301 14.0067 - 113 HS14 16 PHGY H11 113 0.377699 1.0080 - 114 CPos 16 PHGY C2 114 0.354699 12.0110 - 115 HC 16 PHGY H3 115 0.025699 1.0080 - 116 HC 16 PHGY H4 116 0.025699 1.0080 - 117 C 16 PHGY C1 117 -0.036301 12.0110 - 118 HC 16 PHGY H1 118 0.065699 1.0080 - 119 HC 16 PHGY H2 119 0.065699 1.0080 - 120 HS14 17 PHGY H12 120 0.377699 1.0080 - 121 NPri 17 PHGY N2 121 -1.036301 14.0067 - 122 HS14 17 PHGY H11 122 0.377699 1.0080 - 123 CPos 17 PHGY C2 123 0.354699 12.0110 - 124 HC 17 PHGY H3 124 0.025699 1.0080 - 125 HC 17 PHGY H4 125 0.025699 1.0080 - 126 C 17 PHGY C1 126 -0.036301 12.0110 - 127 HC 17 PHGY H1 127 0.065699 1.0080 - 128 HC 17 PHGY H2 128 0.065699 1.0080 - 129 HS14 18 PHGY H12 129 0.377473 1.0080 - 130 NPri 18 PHGY N2 130 -1.036527 14.0067 - 131 HS14 18 PHGY H11 131 0.377473 1.0080 - 132 CPos 18 PHGY C2 132 0.354473 12.0110 - 133 HC 18 PHGY H3 133 0.025473 1.0080 - 134 HC 18 PHGY H4 134 0.025473 1.0080 - 135 C 18 PHGY C1 135 -0.036527 12.0110 - 136 HC 18 PHGY H1 136 0.065473 1.0080 - 137 HC 18 PHGY H2 137 0.065473 1.0080 - 138 HS14 19 PHGY H12 138 0.377437 1.0080 - 139 NPri 19 PHGY N2 139 -1.036563 14.0067 - 140 HS14 19 PHGY H11 140 0.377437 1.0080 - 141 CPos 19 PHGY C2 141 0.354437 12.0110 - 142 HC 19 PHGY H3 142 0.025437 1.0080 - 143 HC 19 PHGY H4 143 0.025437 1.0080 - 144 C 19 PHGY C1 144 -0.036563 12.0110 - 145 HC 19 PHGY H1 145 0.065437 1.0080 - 146 HC 19 PHGY H2 146 0.065437 1.0080 - 147 HS14 20 PHGY H12 147 0.377718 1.0080 - 148 NPri 20 PHGY N2 148 -1.036282 14.0067 - 149 HS14 20 PHGY H11 149 0.377718 1.0080 - 150 CPos 20 PHGY C2 150 0.354718 12.0110 - 151 HC 20 PHGY H3 151 0.025718 1.0080 - 152 HC 20 PHGY H4 152 0.025718 1.0080 - 153 C 20 PHGY C1 153 -0.036282 12.0110 - 154 HC 20 PHGY H1 154 0.065718 1.0080 - 155 HC 20 PHGY H2 155 0.065718 1.0080 - 156 HS14 21 PHGY H12 156 0.377738 1.0080 - 157 NPri 21 PHGY N2 157 -1.036262 14.0067 - 158 HS14 21 PHGY H11 158 0.377738 1.0080 - 159 CPos 21 PHGY C2 159 0.354738 12.0110 - 160 HC 21 PHGY H3 160 0.025738 1.0080 - 161 HC 21 PHGY H4 161 0.025738 1.0080 - 162 C 21 PHGY C1 162 -0.036262 12.0110 - 163 HC 21 PHGY H1 163 0.065738 1.0080 - 164 HC 21 PHGY H2 164 0.065738 1.0080 - 165 HS14 22 PHGY H12 165 0.377702 1.0080 - 166 NPri 22 PHGY N2 166 -1.036298 14.0067 - 167 HS14 22 PHGY H11 167 0.377702 1.0080 - 168 CPos 22 PHGY C2 168 0.354702 12.0110 - 169 HC 22 PHGY H3 169 0.025702 1.0080 - 170 HC 22 PHGY H4 170 0.025702 1.0080 - 171 C 22 PHGY C1 171 -0.036298 12.0110 - 172 HC 22 PHGY H1 172 0.065702 1.0080 - 173 HC 22 PHGY H2 173 0.065702 1.0080 - 174 HS14 23 PHGY H12 174 0.377738 1.0080 - 175 NPri 23 PHGY N2 175 -1.036262 14.0067 - 176 HS14 23 PHGY H11 176 0.377738 1.0080 - 177 CPos 23 PHGY C2 177 0.354738 12.0110 - 178 HC 23 PHGY H3 178 0.025738 1.0080 - 179 HC 23 PHGY H4 179 0.025738 1.0080 - 180 C 23 PHGY C1 180 -0.036262 12.0110 - 181 HC 23 PHGY H1 181 0.065738 1.0080 - 182 HC 23 PHGY H2 182 0.065738 1.0080 - 183 HS14 24 PHGY H12 183 0.377753 1.0080 - 184 NPri 24 PHGY N2 184 -1.036247 14.0067 - 185 HS14 24 PHGY H11 185 0.377753 1.0080 - 186 CPos 24 PHGY C2 186 0.354753 12.0110 - 187 HC 24 PHGY H3 187 0.025753 1.0080 - 188 HC 24 PHGY H4 188 0.025753 1.0080 - 189 C 24 PHGY C1 189 -0.036247 12.0110 - 190 HC 24 PHGY H1 190 0.065753 1.0080 - 191 HC 24 PHGY H2 191 0.065753 1.0080 - 192 HS14 25 PHGY H12 192 0.377718 1.0080 - 193 NPri 25 PHGY N2 193 -1.036282 14.0067 - 194 HS14 25 PHGY H11 194 0.377718 1.0080 - 195 CPos 25 PHGY C2 195 0.354718 12.0110 - 196 HC 25 PHGY H3 196 0.025718 1.0080 - 197 HC 25 PHGY H4 197 0.025718 1.0080 - 198 C 25 PHGY C1 198 -0.036282 12.0110 - 199 HC 25 PHGY H1 199 0.065718 1.0080 - 200 HC 25 PHGY H2 200 0.065718 1.0080 - 201 HS14 26 PHGY H12 201 0.377683 1.0080 - 202 NPri 26 PHGY N2 202 -1.036317 14.0067 - 203 HS14 26 PHGY H11 203 0.377683 1.0080 - 204 CPos 26 PHGY C2 204 0.354683 12.0110 - 205 HC 26 PHGY H3 205 0.025683 1.0080 - 206 HC 26 PHGY H4 206 0.025683 1.0080 - 207 C 26 PHGY C1 207 -0.036317 12.0110 - 208 HC 26 PHGY H1 208 0.065683 1.0080 - 209 HC 26 PHGY H2 209 0.065683 1.0080 - 210 HS14 27 PHGY H12 210 0.377663 1.0080 - 211 NPri 27 PHGY N2 211 -1.036337 14.0067 - 212 HS14 27 PHGY H11 212 0.377663 1.0080 - 213 CPos 27 PHGY C2 213 0.354663 12.0110 - 214 HC 27 PHGY H3 214 0.025663 1.0080 - 215 HC 27 PHGY H4 215 0.025663 1.0080 - 216 C 27 PHGY C1 216 -0.036337 12.0110 - 217 HC 27 PHGY H1 217 0.065663 1.0080 - 218 HC 27 PHGY H2 218 0.065663 1.0080 - 219 HS14 28 PHGY H12 219 0.377683 1.0080 - 220 NPri 28 PHGY N2 220 -1.036317 14.0067 - 221 HS14 28 PHGY H11 221 0.377683 1.0080 - 222 CPos 28 PHGY C2 222 0.354683 12.0110 - 223 HC 28 PHGY H3 223 0.025683 1.0080 - 224 HC 28 PHGY H4 224 0.025683 1.0080 - 225 C 28 PHGY C1 225 -0.036317 12.0110 - 226 HC 28 PHGY H1 226 0.065683 1.0080 - 227 HC 28 PHGY H2 227 0.065683 1.0080 - 228 HS14 29 PHGY H12 228 0.375851 1.0080 - 229 NPri 29 PHGY N2 229 -1.038149 14.0067 - 230 HS14 29 PHGY H11 230 0.375851 1.0080 - 231 CPos 29 PHGY C2 231 0.352851 12.0110 - 232 HC 29 PHGY H3 232 0.023851 1.0080 - 233 HC 29 PHGY H4 233 0.023851 1.0080 - 234 C 29 PHGY C1 234 -0.038149 12.0110 - 235 HC 29 PHGY H1 235 0.063851 1.0080 - 236 HC 29 PHGY H2 236 0.063851 1.0080 + 86 CPos 13 BB6C C6 86 -0.137307 12.0110 + 87 HC 13 BB6C H13 87 0.116693 1.0080 + 88 HC 13 BB6C H14 88 0.116693 1.0080 + 89 CPos 13 BB6C C5 89 0.142693 12.0110 + 90 HC 13 BB6C H11 90 0.060693 1.0080 + 91 HC 13 BB6C H12 91 0.060693 1.0080 + 92 NTer 13 BB6C N1 92 -0.590307 14.0067 + 93 HS14 14 PHGY H12 93 0.376960 1.0080 + 94 NPri 14 PHGY N2 94 -1.037040 14.0067 + 95 HS14 14 PHGY H11 95 0.376960 1.0080 + 96 CPos 14 PHGY C2 96 0.353960 12.0110 + 97 HC 14 PHGY H3 97 0.024960 1.0080 + 98 HC 14 PHGY H4 98 0.024960 1.0080 + 99 C 14 PHGY C1 99 -0.037040 12.0110 + 100 HC 14 PHGY H1 100 0.064960 1.0080 + 101 HC 14 PHGY H2 101 0.064960 1.0080 + 102 HS14 15 PHGY H12 102 0.377742 1.0080 + 103 NPri 15 PHGY N2 103 -1.036258 14.0067 + 104 HS14 15 PHGY H11 104 0.377742 1.0080 + 105 CPos 15 PHGY C2 105 0.354742 12.0110 + 106 HC 15 PHGY H3 106 0.025742 1.0080 + 107 HC 15 PHGY H4 107 0.025742 1.0080 + 108 C 15 PHGY C1 108 -0.036258 12.0110 + 109 HC 15 PHGY H1 109 0.065742 1.0080 + 110 HC 15 PHGY H2 110 0.065742 1.0080 + 111 HS14 16 PHGY H12 111 0.377761 1.0080 + 112 NPri 16 PHGY N2 112 -1.036239 14.0067 + 113 HS14 16 PHGY H11 113 0.377761 1.0080 + 114 CPos 16 PHGY C2 114 0.354761 12.0110 + 115 HC 16 PHGY H3 115 0.025761 1.0080 + 116 HC 16 PHGY H4 116 0.025761 1.0080 + 117 C 16 PHGY C1 117 -0.036239 12.0110 + 118 HC 16 PHGY H1 118 0.065761 1.0080 + 119 HC 16 PHGY H2 119 0.065761 1.0080 + 120 HS14 17 PHGY H12 120 0.377712 1.0080 + 121 NPri 17 PHGY N2 121 -1.036288 14.0067 + 122 HS14 17 PHGY H11 122 0.377712 1.0080 + 123 CPos 17 PHGY C2 123 0.354712 12.0110 + 124 HC 17 PHGY H3 124 0.025712 1.0080 + 125 HC 17 PHGY H4 125 0.025712 1.0080 + 126 C 17 PHGY C1 126 -0.036288 12.0110 + 127 HC 17 PHGY H1 127 0.065712 1.0080 + 128 HC 17 PHGY H2 128 0.065712 1.0080 + 129 HS14 18 PHGY H12 129 0.377663 1.0080 + 130 NPri 18 PHGY N2 130 -1.036337 14.0067 + 131 HS14 18 PHGY H11 131 0.377663 1.0080 + 132 CPos 18 PHGY C2 132 0.354663 12.0110 + 133 HC 18 PHGY H3 133 0.025663 1.0080 + 134 HC 18 PHGY H4 134 0.025663 1.0080 + 135 C 18 PHGY C1 135 -0.036337 12.0110 + 136 HC 18 PHGY H1 136 0.065663 1.0080 + 137 HC 18 PHGY H2 137 0.065663 1.0080 + 138 HS14 19 PHGY H12 138 0.377490 1.0080 + 139 NPri 19 PHGY N2 139 -1.036510 14.0067 + 140 HS14 19 PHGY H11 140 0.377490 1.0080 + 141 CPos 19 PHGY C2 141 0.354490 12.0110 + 142 HC 19 PHGY H3 142 0.025490 1.0080 + 143 HC 19 PHGY H4 143 0.025490 1.0080 + 144 C 19 PHGY C1 144 -0.036510 12.0110 + 145 HC 19 PHGY H1 145 0.065490 1.0080 + 146 HC 19 PHGY H2 146 0.065490 1.0080 + 147 HS14 20 PHGY H12 147 0.377490 1.0080 + 148 NPri 20 PHGY N2 148 -1.036510 14.0067 + 149 HS14 20 PHGY H11 149 0.377490 1.0080 + 150 CPos 20 PHGY C2 150 0.354490 12.0110 + 151 HC 20 PHGY H3 151 0.025490 1.0080 + 152 HC 20 PHGY H4 152 0.025490 1.0080 + 153 C 20 PHGY C1 153 -0.036510 12.0110 + 154 HC 20 PHGY H1 154 0.065490 1.0080 + 155 HC 20 PHGY H2 155 0.065490 1.0080 + 156 HS14 21 PHGY H12 156 0.377693 1.0080 + 157 NPri 21 PHGY N2 157 -1.036307 14.0067 + 158 HS14 21 PHGY H11 158 0.377693 1.0080 + 159 CPos 21 PHGY C2 159 0.354693 12.0110 + 160 HC 21 PHGY H3 160 0.025693 1.0080 + 161 HC 21 PHGY H4 161 0.025693 1.0080 + 162 C 21 PHGY C1 162 -0.036307 12.0110 + 163 HC 21 PHGY H1 163 0.065693 1.0080 + 164 HC 21 PHGY H2 164 0.065693 1.0080 + 165 HS14 22 PHGY H12 165 0.377722 1.0080 + 166 NPri 22 PHGY N2 166 -1.036278 14.0067 + 167 HS14 22 PHGY H11 167 0.377722 1.0080 + 168 CPos 22 PHGY C2 168 0.354722 12.0110 + 169 HC 22 PHGY H3 169 0.025722 1.0080 + 170 HC 22 PHGY H4 170 0.025722 1.0080 + 171 C 22 PHGY C1 171 -0.036278 12.0110 + 172 HC 22 PHGY H1 172 0.065722 1.0080 + 173 HC 22 PHGY H2 173 0.065722 1.0080 + 174 HS14 23 PHGY H12 174 0.377742 1.0080 + 175 NPri 23 PHGY N2 175 -1.036258 14.0067 + 176 HS14 23 PHGY H11 176 0.377742 1.0080 + 177 CPos 23 PHGY C2 177 0.354742 12.0110 + 178 HC 23 PHGY H3 178 0.025742 1.0080 + 179 HC 23 PHGY H4 179 0.025742 1.0080 + 180 C 23 PHGY C1 180 -0.036258 12.0110 + 181 HC 23 PHGY H1 181 0.065742 1.0080 + 182 HC 23 PHGY H2 182 0.065742 1.0080 + 183 HS14 24 PHGY H12 183 0.377732 1.0080 + 184 NPri 24 PHGY N2 184 -1.036268 14.0067 + 185 HS14 24 PHGY H11 185 0.377732 1.0080 + 186 CPos 24 PHGY C2 186 0.354732 12.0110 + 187 HC 24 PHGY H3 187 0.025732 1.0080 + 188 HC 24 PHGY H4 188 0.025732 1.0080 + 189 C 24 PHGY C1 189 -0.036268 12.0110 + 190 HC 24 PHGY H1 190 0.065732 1.0080 + 191 HC 24 PHGY H2 191 0.065732 1.0080 + 192 HS14 25 PHGY H12 192 0.377712 1.0080 + 193 NPri 25 PHGY N2 193 -1.036288 14.0067 + 194 HS14 25 PHGY H11 194 0.377712 1.0080 + 195 CPos 25 PHGY C2 195 0.354712 12.0110 + 196 HC 25 PHGY H3 196 0.025712 1.0080 + 197 HC 25 PHGY H4 197 0.025712 1.0080 + 198 C 25 PHGY C1 198 -0.036288 12.0110 + 199 HC 25 PHGY H1 199 0.065712 1.0080 + 200 HC 25 PHGY H2 200 0.065712 1.0080 + 201 HS14 26 PHGY H12 201 0.377742 1.0080 + 202 NPri 26 PHGY N2 202 -1.036258 14.0067 + 203 HS14 26 PHGY H11 203 0.377742 1.0080 + 204 CPos 26 PHGY C2 204 0.354742 12.0110 + 205 HC 26 PHGY H3 205 0.025742 1.0080 + 206 HC 26 PHGY H4 206 0.025742 1.0080 + 207 C 26 PHGY C1 207 -0.036258 12.0110 + 208 HC 26 PHGY H1 208 0.065742 1.0080 + 209 HC 26 PHGY H2 209 0.065742 1.0080 + 210 HS14 27 PHGY H12 210 0.377732 1.0080 + 211 NPri 27 PHGY N2 211 -1.036268 14.0067 + 212 HS14 27 PHGY H11 212 0.377732 1.0080 + 213 CPos 27 PHGY C2 213 0.354732 12.0110 + 214 HC 27 PHGY H3 214 0.025732 1.0080 + 215 HC 27 PHGY H4 215 0.025732 1.0080 + 216 C 27 PHGY C1 216 -0.036268 12.0110 + 217 HC 27 PHGY H1 217 0.065732 1.0080 + 218 HC 27 PHGY H2 218 0.065732 1.0080 + 219 HS14 28 PHGY H12 219 0.377510 1.0080 + 220 NPri 28 PHGY N2 220 -1.036490 14.0067 + 221 HS14 28 PHGY H11 221 0.377510 1.0080 + 222 CPos 28 PHGY C2 222 0.354510 12.0110 + 223 HC 28 PHGY H3 223 0.025510 1.0080 + 224 HC 28 PHGY H4 224 0.025510 1.0080 + 225 C 28 PHGY C1 225 -0.036490 12.0110 + 226 HC 28 PHGY H1 226 0.065510 1.0080 + 227 HC 28 PHGY H2 227 0.065510 1.0080 + 228 HS14 29 PHGY H12 228 0.375659 1.0080 + 229 NPri 29 PHGY N2 229 -1.038342 14.0067 + 230 HS14 29 PHGY H11 230 0.375659 1.0080 + 231 CPos 29 PHGY C2 231 0.352658 12.0110 + 232 HC 29 PHGY H3 232 0.023658 1.0080 + 233 HC 29 PHGY H4 233 0.023658 1.0080 + 234 C 29 PHGY C1 234 -0.038342 12.0110 + 235 HC 29 PHGY H1 235 0.063658 1.0080 + 236 HC 29 PHGY H2 236 0.063658 1.0080 [ bonds ] 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"exclusions": [], "preamble": [";----------------------------TITLE -----------------------------------------------------------------------------------------", "; None", ";", "; This file was generated at 14:09 on 2024-12-06 by", ";", "; Automatic Topology Builder", ";", "; REVISION 2024-11-20 12:06:25", ";---------------------------------------------------------------------------------------------------------------------------", "; Authors : Martin Stroet, Bertrand Caron, Alpeshkumar K. Malde, Thomas Lee, Alan E. Mark", ";", "; Institute : Molecular Dynamics group,", "; School of Chemistry and Molecular Biosciences (SCMB),", "; The University of Queensland, QLD 4072, Australia", "; URL : https://atb.uq.edu.au", "; Citations : 1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, Nair PC, Oostenbrink C, Mark AE.", "; An Automated force field Topology Builder (ATB) and repository: version 1.0.", "; Journal of Chemical Theory and Computation, 2011, 7, 4026-4037.", "; 2. Stroet M, Caron B, Visscher K, Geerke D, Malde AK, Mark AE.", "; Automated Topology Builder version 3.0: Prediction of solvation free enthalpies in water and hexane.", "; DOI:10.1021/acs.jctc.8b00768", ";", "; Disclaimer :", "; While every effort has been made to ensure the accuracy and validity of parameters provided below", "; the assignment of parameters is being based on an automated procedure combining data provided by a", "; given user as well as calculations performed using third party software. They are provided as a guide.", "; The authors of the ATB cannot guarantee that the parameters are complete or that the parameters provided", "; are appropriate for use in any specific application. Users are advised to treat these parameters with discretion", "; and to perform additional validation tests for their specific application if required. Neither the authors", "; of the ATB or The University of Queensland except any responsibly for how the parameters may be used.", ";", "; Release notes and warnings:", "; (1) The topology is based on a set of atomic coordinates and other data provided by the user after", "; after quantum mechanical optimization of the structure using different levels of theory depending on", "; the nature of the molecule.", "; (2) In some cases the automatic bond, bond angle and dihedral type assignment is ambiguous.", "; In these cases alternative type codes are provided at the end of the line.", "; (3) While bonded parameters are taken where possible from the nominated force field non-standard bond, angle and dihedral", "; type code may be incorporated in cases where an exact match could not be found. These are marked as \"non-standard\"", "; or \"uncertain\" in comments.", "; (4) In some cases it is not possible to assign an appropriate parameter automatically. \"%%\" is used as a place holder", "; for those fields that could not be determined automatically. The parameters in these fields must be assigned manually", "; before the file can be used.", ";---------------------------------------------------------------------------------------------------------------------------", "; Input Structure : 6HTJ", "; Output : ALL ATOM topology", ";\tUse in conjunction with the corresponding all atom PDB file.", ";---------------------------------------------------------------------------------------------------------------------------", "; Citing this topology file", "; ATB molid: 1746623", "; ATB Topology Hash: f4741", ";---------------------------------------------------------------------------------------------------------------------------", "; Final Topology Generation was performed using:", "; A B3LYP/6-31G* optimized geometry.", "; Bonded and van der Waals parameters were taken from the GROMOS 54A7 parameter set.", "; Initial charges were estimated using the ESP method of Merz-Kollman.", "; Final charges and charge groups were generated by method described in the ATB paper.", "; If required, additional bonded parameters were generated from a Hessian matrix calculated at the B3LYP/6-31G* level of theory.", ";---------------------------------------------------------------------------------------------------------------------------", ";", ";"], "moleculetype": {"name": "6HTJ", "nrexcl": 3}}, "junctions": []} \ No newline at end of file +{"topology": {"atoms": [{"atom_id": 1, "atom_type": "CPos", "residue_id": 1, "residue_name": "6HTJ", "atom_name": "C6", "charge_group_num": 16, "partial_charge": 0.021840000000000002, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 2, "atom_type": "HC", "residue_id": 1, "residue_name": "6HTJ", "atom_name": "H13", "charge_group_num": 17, "partial_charge": 0.07884, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 3, "atom_type": "HC", "residue_id": 1, "residue_name": "6HTJ", "atom_name": "H14", "charge_group_num": 18, "partial_charge": 0.07884, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 4, "atom_type": "CPos", "residue_id": 1, "residue_name": "6HTJ", "atom_name": "C5", "charge_group_num": 19, "partial_charge": 0.021840000000000002, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 5, "atom_type": "HC", "residue_id": 1, "residue_name": "6HTJ", "atom_name": "H11", "charge_group_num": 20, "partial_charge": 0.07884, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 6, "atom_type": "HC", "residue_id": 1, "residue_name": "6HTJ", "atom_name": "H12", "charge_group_num": 21, "partial_charge": 0.07884, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 7, "atom_type": "CPos", "residue_id": 2, "residue_name": "BB6C", "atom_name": "C6", "charge_group_num": 10, "partial_charge": -0.13802, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 8, "atom_type": "HC", "residue_id": 2, "residue_name": "BB6C", "atom_name": "H13", "charge_group_num": 11, "partial_charge": 0.11598, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 9, "atom_type": "HC", "residue_id": 2, "residue_name": "BB6C", "atom_name": "H14", "charge_group_num": 12, "partial_charge": 0.11598, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 10, "atom_type": "CPos", "residue_id": 2, "residue_name": "BB6C", "atom_name": "C5", "charge_group_num": 13, "partial_charge": 0.14198000000000002, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 11, "atom_type": "HC", "residue_id": 2, "residue_name": "BB6C", "atom_name": "H11", "charge_group_num": 14, "partial_charge": 0.05998, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 12, "atom_type": "HC", "residue_id": 2, "residue_name": "BB6C", "atom_name": "H12", "charge_group_num": 15, "partial_charge": 0.05998, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 13, "atom_type": "NTer", "residue_id": 1, "residue_name": "6HTJ", "atom_name": "N2", "charge_group_num": 8, "partial_charge": -0.5541600000000001, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 14, "atom_type": "CPos", "residue_id": 3, "residue_name": "BB6C", "atom_name": "C6", "charge_group_num": 10, "partial_charge": -0.13772, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 15, "atom_type": "HC", "residue_id": 3, "residue_name": "BB6C", "atom_name": "H13", "charge_group_num": 11, "partial_charge": 0.11628000000000001, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 16, "atom_type": "HC", "residue_id": 3, "residue_name": "BB6C", "atom_name": "H14", "charge_group_num": 12, "partial_charge": 0.11628000000000001, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 17, "atom_type": "CPos", "residue_id": 3, "residue_name": "BB6C", "atom_name": "C5", 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101, "pair_type": 1}, {"atom_a": 97, "atom_b": 99, "pair_type": 1}, {"atom_a": 97, "atom_b": 100, "pair_type": 1}, {"atom_a": 99, "atom_b": 103, "pair_type": 1}, {"atom_a": 99, "atom_b": 102, "pair_type": 1}, {"atom_a": 100, "atom_b": 103, "pair_type": 1}, {"atom_a": 100, "atom_b": 102, "pair_type": 1}, {"atom_a": 104, "atom_b": 110, "pair_type": 1}, {"atom_a": 104, "atom_b": 109, "pair_type": 1}, {"atom_a": 104, "atom_b": 108, "pair_type": 1}, {"atom_a": 105, "atom_b": 111, "pair_type": 1}, {"atom_a": 105, "atom_b": 112, "pair_type": 1}, {"atom_a": 106, "atom_b": 108, "pair_type": 1}, {"atom_a": 106, "atom_b": 110, "pair_type": 1}, {"atom_a": 106, "atom_b": 109, "pair_type": 1}, {"atom_a": 108, "atom_b": 112, "pair_type": 1}, {"atom_a": 108, "atom_b": 111, "pair_type": 1}, {"atom_a": 109, "atom_b": 111, "pair_type": 1}, {"atom_a": 109, "atom_b": 112, "pair_type": 1}, {"atom_a": 113, "atom_b": 119, "pair_type": 1}, {"atom_a": 113, "atom_b": 117, "pair_type": 1}, {"atom_a": 113, "atom_b": 118, "pair_type": 1}, {"atom_a": 114, "atom_b": 121, "pair_type": 1}, {"atom_a": 114, "atom_b": 120, "pair_type": 1}, {"atom_a": 115, "atom_b": 119, "pair_type": 1}, {"atom_a": 115, "atom_b": 118, "pair_type": 1}, {"atom_a": 115, "atom_b": 117, "pair_type": 1}, {"atom_a": 117, "atom_b": 120, "pair_type": 1}, {"atom_a": 117, "atom_b": 121, "pair_type": 1}, {"atom_a": 118, "atom_b": 120, "pair_type": 1}, {"atom_a": 118, "atom_b": 121, "pair_type": 1}, {"atom_a": 122, "atom_b": 127, "pair_type": 1}, {"atom_a": 122, "atom_b": 128, "pair_type": 1}, {"atom_a": 122, "atom_b": 126, "pair_type": 1}, {"atom_a": 123, "atom_b": 129, "pair_type": 1}, {"atom_a": 123, "atom_b": 130, "pair_type": 1}, {"atom_a": 124, "atom_b": 126, "pair_type": 1}, {"atom_a": 124, "atom_b": 128, "pair_type": 1}, {"atom_a": 124, "atom_b": 127, "pair_type": 1}, {"atom_a": 126, "atom_b": 130, "pair_type": 1}, {"atom_a": 126, "atom_b": 129, "pair_type": 1}, {"atom_a": 127, "atom_b": 129, "pair_type": 1}, {"atom_a": 127, "atom_b": 130, "pair_type": 1}, {"atom_a": 131, "atom_b": 137, "pair_type": 1}, {"atom_a": 131, "atom_b": 136, "pair_type": 1}, {"atom_a": 131, "atom_b": 135, "pair_type": 1}, {"atom_a": 132, "atom_b": 139, "pair_type": 1}, {"atom_a": 132, "atom_b": 138, "pair_type": 1}, {"atom_a": 133, "atom_b": 135, "pair_type": 1}, {"atom_a": 133, "atom_b": 137, "pair_type": 1}, {"atom_a": 133, "atom_b": 136, "pair_type": 1}, {"atom_a": 135, "atom_b": 138, "pair_type": 1}, {"atom_a": 135, "atom_b": 139, "pair_type": 1}, {"atom_a": 136, "atom_b": 139, "pair_type": 1}, {"atom_a": 136, "atom_b": 138, "pair_type": 1}, {"atom_a": 141, "atom_b": 145, "pair_type": 1}, {"atom_a": 141, "atom_b": 146, "pair_type": 1}, {"atom_a": 141, "atom_b": 147, "pair_type": 1}, {"atom_a": 142, "atom_b": 149, "pair_type": 1}, {"atom_a": 142, "atom_b": 148, "pair_type": 1}, {"atom_a": 143, "atom_b": 146, "pair_type": 1}, {"atom_a": 143, "atom_b": 145, "pair_type": 1}, {"atom_a": 143, "atom_b": 147, "pair_type": 1}, {"atom_a": 145, "atom_b": 149, "pair_type": 1}, {"atom_a": 145, "atom_b": 148, "pair_type": 1}, {"atom_a": 146, "atom_b": 148, "pair_type": 1}, {"atom_a": 146, "atom_b": 149, "pair_type": 1}, {"atom_a": 151, "atom_b": 157, "pair_type": 1}, {"atom_a": 151, "atom_b": 156, "pair_type": 1}, {"atom_a": 151, "atom_b": 155, "pair_type": 1}, {"atom_a": 152, "atom_b": 158, "pair_type": 1}, {"atom_a": 152, "atom_b": 159, "pair_type": 1}, {"atom_a": 153, "atom_b": 157, "pair_type": 1}, {"atom_a": 153, "atom_b": 155, "pair_type": 1}, {"atom_a": 153, "atom_b": 156, "pair_type": 1}, {"atom_a": 155, "atom_b": 158, "pair_type": 1}, {"atom_a": 155, "atom_b": 159, "pair_type": 1}, {"atom_a": 156, "atom_b": 159, "pair_type": 1}, {"atom_a": 156, "atom_b": 158, "pair_type": 1}, {"atom_a": 161, "atom_b": 166, "pair_type": 1}, {"atom_a": 161, "atom_b": 167, "pair_type": 1}, {"atom_a": 161, "atom_b": 165, "pair_type": 1}, {"atom_a": 162, "atom_b": 169, "pair_type": 1}, {"atom_a": 162, "atom_b": 168, "pair_type": 1}, {"atom_a": 163, "atom_b": 166, "pair_type": 1}, {"atom_a": 163, "atom_b": 167, "pair_type": 1}, {"atom_a": 163, "atom_b": 165, "pair_type": 1}, {"atom_a": 165, "atom_b": 169, "pair_type": 1}, {"atom_a": 165, "atom_b": 168, "pair_type": 1}, {"atom_a": 166, "atom_b": 169, "pair_type": 1}, {"atom_a": 166, "atom_b": 168, "pair_type": 1}, {"atom_a": 170, "atom_b": 176, "pair_type": 1}, {"atom_a": 170, "atom_b": 174, "pair_type": 1}, {"atom_a": 170, "atom_b": 175, "pair_type": 1}, {"atom_a": 171, "atom_b": 177, "pair_type": 1}, {"atom_a": 171, "atom_b": 178, "pair_type": 1}, {"atom_a": 172, "atom_b": 174, "pair_type": 1}, {"atom_a": 172, "atom_b": 175, "pair_type": 1}, {"atom_a": 172, "atom_b": 176, "pair_type": 1}, {"atom_a": 174, "atom_b": 178, "pair_type": 1}, {"atom_a": 174, "atom_b": 177, "pair_type": 1}, {"atom_a": 175, "atom_b": 177, "pair_type": 1}, {"atom_a": 175, "atom_b": 178, "pair_type": 1}, {"atom_a": 180, "atom_b": 186, "pair_type": 1}, {"atom_a": 180, "atom_b": 184, "pair_type": 1}, {"atom_a": 180, "atom_b": 185, "pair_type": 1}, {"atom_a": 181, "atom_b": 188, "pair_type": 1}, {"atom_a": 181, "atom_b": 187, "pair_type": 1}, {"atom_a": 182, "atom_b": 185, "pair_type": 1}, {"atom_a": 182, "atom_b": 186, "pair_type": 1}, {"atom_a": 182, "atom_b": 184, "pair_type": 1}, {"atom_a": 184, "atom_b": 188, "pair_type": 1}, {"atom_a": 184, "atom_b": 187, "pair_type": 1}, {"atom_a": 185, "atom_b": 188, "pair_type": 1}, {"atom_a": 185, "atom_b": 187, "pair_type": 1}, {"atom_a": 190, "atom_b": 194, "pair_type": 1}, {"atom_a": 190, "atom_b": 196, "pair_type": 1}, {"atom_a": 190, "atom_b": 195, "pair_type": 1}, {"atom_a": 191, "atom_b": 198, "pair_type": 1}, {"atom_a": 191, "atom_b": 197, "pair_type": 1}, {"atom_a": 192, "atom_b": 196, "pair_type": 1}, {"atom_a": 192, "atom_b": 195, "pair_type": 1}, {"atom_a": 192, "atom_b": 194, "pair_type": 1}, {"atom_a": 194, "atom_b": 197, "pair_type": 1}, {"atom_a": 194, "atom_b": 198, "pair_type": 1}, {"atom_a": 195, "atom_b": 197, "pair_type": 1}, {"atom_a": 195, "atom_b": 198, "pair_type": 1}, {"atom_a": 199, "atom_b": 204, "pair_type": 1}, {"atom_a": 199, "atom_b": 203, "pair_type": 1}, {"atom_a": 199, "atom_b": 205, "pair_type": 1}, {"atom_a": 200, "atom_b": 206, "pair_type": 1}, {"atom_a": 200, "atom_b": 207, "pair_type": 1}, {"atom_a": 201, "atom_b": 203, "pair_type": 1}, {"atom_a": 201, "atom_b": 205, "pair_type": 1}, {"atom_a": 201, "atom_b": 204, "pair_type": 1}, {"atom_a": 203, "atom_b": 207, "pair_type": 1}, {"atom_a": 203, "atom_b": 206, "pair_type": 1}, {"atom_a": 204, "atom_b": 207, "pair_type": 1}, {"atom_a": 204, "atom_b": 206, "pair_type": 1}, {"atom_a": 209, "atom_b": 215, "pair_type": 1}, {"atom_a": 209, "atom_b": 214, "pair_type": 1}, {"atom_a": 209, "atom_b": 213, "pair_type": 1}, {"atom_a": 210, "atom_b": 216, "pair_type": 1}, {"atom_a": 210, "atom_b": 217, "pair_type": 1}, {"atom_a": 211, "atom_b": 215, "pair_type": 1}, {"atom_a": 211, "atom_b": 213, "pair_type": 1}, {"atom_a": 211, "atom_b": 214, "pair_type": 1}, {"atom_a": 213, "atom_b": 216, "pair_type": 1}, {"atom_a": 213, "atom_b": 217, "pair_type": 1}, {"atom_a": 214, "atom_b": 216, "pair_type": 1}, {"atom_a": 214, "atom_b": 217, "pair_type": 1}, {"atom_a": 219, "atom_b": 225, "pair_type": 1}, {"atom_a": 219, "atom_b": 224, "pair_type": 1}, {"atom_a": 219, "atom_b": 223, "pair_type": 1}, {"atom_a": 220, "atom_b": 226, "pair_type": 1}, {"atom_a": 220, "atom_b": 227, "pair_type": 1}, {"atom_a": 221, "atom_b": 225, "pair_type": 1}, {"atom_a": 221, "atom_b": 224, "pair_type": 1}, {"atom_a": 221, "atom_b": 223, "pair_type": 1}, {"atom_a": 223, "atom_b": 226, "pair_type": 1}, {"atom_a": 223, "atom_b": 227, "pair_type": 1}, {"atom_a": 224, "atom_b": 226, "pair_type": 1}, {"atom_a": 224, "atom_b": 227, "pair_type": 1}, {"atom_a": 229, "atom_b": 234, "pair_type": 1}, {"atom_a": 229, "atom_b": 235, "pair_type": 1}, {"atom_a": 229, "atom_b": 233, "pair_type": 1}, {"atom_a": 230, "atom_b": 236, "pair_type": 1}, {"atom_a": 230, "atom_b": 237, "pair_type": 1}, {"atom_a": 231, "atom_b": 233, "pair_type": 1}, {"atom_a": 231, "atom_b": 234, "pair_type": 1}, {"atom_a": 231, "atom_b": 235, "pair_type": 1}, {"atom_a": 233, "atom_b": 237, "pair_type": 1}, {"atom_a": 233, "atom_b": 236, "pair_type": 1}, {"atom_a": 234, "atom_b": 237, "pair_type": 1}, {"atom_a": 234, "atom_b": 236, "pair_type": 1}], "exclusions": [], "preamble": [";----------------------------TITLE -----------------------------------------------------------------------------------------", "; None", ";", "; This file was generated at 14:09 on 2024-12-06 by", ";", "; Automatic Topology Builder", ";", "; REVISION 2024-11-20 12:06:25", ";---------------------------------------------------------------------------------------------------------------------------", "; Authors : Martin Stroet, Bertrand Caron, Alpeshkumar K. Malde, Thomas Lee, Alan E. Mark", ";", "; Institute : Molecular Dynamics group,", "; School of Chemistry and Molecular Biosciences (SCMB),", "; The University of Queensland, QLD 4072, Australia", "; URL : https://atb.uq.edu.au", "; Citations : 1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, Nair PC, Oostenbrink C, Mark AE.", "; An Automated force field Topology Builder (ATB) and repository: version 1.0.", "; Journal of Chemical Theory and Computation, 2011, 7, 4026-4037.", "; 2. Stroet M, Caron B, Visscher K, Geerke D, Malde AK, Mark AE.", "; Automated Topology Builder version 3.0: Prediction of solvation free enthalpies in water and hexane.", "; DOI:10.1021/acs.jctc.8b00768", ";", "; Disclaimer :", "; While every effort has been made to ensure the accuracy and validity of parameters provided below", "; the assignment of parameters is being based on an automated procedure combining data provided by a", "; given user as well as calculations performed using third party software. They are provided as a guide.", "; The authors of the ATB cannot guarantee that the parameters are complete or that the parameters provided", "; are appropriate for use in any specific application. Users are advised to treat these parameters with discretion", "; and to perform additional validation tests for their specific application if required. Neither the authors", "; of the ATB or The University of Queensland except any responsibly for how the parameters may be used.", ";", "; Release notes and warnings:", "; (1) The topology is based on a set of atomic coordinates and other data provided by the user after", "; after quantum mechanical optimization of the structure using different levels of theory depending on", "; the nature of the molecule.", "; (2) In some cases the automatic bond, bond angle and dihedral type assignment is ambiguous.", "; In these cases alternative type codes are provided at the end of the line.", "; (3) While bonded parameters are taken where possible from the nominated force field non-standard bond, angle and dihedral", "; type code may be incorporated in cases where an exact match could not be found. These are marked as \"non-standard\"", "; or \"uncertain\" in comments.", "; (4) In some cases it is not possible to assign an appropriate parameter automatically. \"%%\" is used as a place holder", "; for those fields that could not be determined automatically. The parameters in these fields must be assigned manually", "; before the file can be used.", ";---------------------------------------------------------------------------------------------------------------------------", "; Input Structure : 6HTJ", "; Output : ALL ATOM topology", ";\tUse in conjunction with the corresponding all atom PDB file.", ";---------------------------------------------------------------------------------------------------------------------------", "; Citing this topology file", "; ATB molid: 1746623", "; ATB Topology Hash: f4741", ";---------------------------------------------------------------------------------------------------------------------------", "; Final Topology Generation was performed using:", "; A B3LYP/6-31G* optimized geometry.", "; Bonded and van der Waals parameters were taken from the GROMOS 54A7 parameter set.", "; Initial charges were estimated using the ESP method of Merz-Kollman.", "; Final charges and charge groups were generated by method described in the ATB paper.", "; If required, additional bonded parameters were generated from a Hessian matrix calculated at the B3LYP/6-31G* level of theory.", ";---------------------------------------------------------------------------------------------------------------------------", ";", ";"], "moleculetype": {"name": "6HTJ", "nrexcl": 3}}, "junctions": []} \ No newline at end of file diff --git a/data_paper_examples/ethylamine_dendrimer.png b/data_paper_examples/ethylamine_dendrimer.png index 02d31de..400fd91 100644 Binary files a/data_paper_examples/ethylamine_dendrimer.png and b/data_paper_examples/ethylamine_dendrimer.png differ diff --git a/data_paper_examples/four_arm_star_overlapped_monomers.itp b/data_paper_examples/four_arm_star_overlapped_monomers.itp index 09555af..0ed2e6e 100644 --- a/data_paper_examples/four_arm_star_overlapped_monomers.itp +++ b/data_paper_examples/four_arm_star_overlapped_monomers.itp @@ -181,186 +181,186 @@ 113 HC 17 45ZJ H3 113 -0.052754 1.0080 [ bonds ] + 1 3 2 0.1090 1.2300e+07 1 2 2 0.1090 1.2300e+07 - 1 4 2 0.1540 4.0057e+06 1 41 2 0.1430 8.1800e+06 - 1 3 2 0.1090 1.2300e+07 + 1 4 2 0.1540 4.0057e+06 + 4 11 2 0.1540 4.0057e+06 4 5 2 0.1540 4.0057e+06 4 8 2 0.1540 4.0057e+06 - 4 11 2 0.1540 4.0057e+06 5 6 2 0.1090 1.2300e+07 5 20 2 0.1430 8.1800e+06 5 7 2 0.1090 1.2300e+07 8 27 2 0.1430 8.1800e+06 8 10 2 0.1090 1.2300e+07 8 9 2 0.1090 1.2300e+07 + 11 34 2 0.1430 8.1800e+06 11 13 2 0.1090 1.2300e+07 11 12 2 0.1090 1.2300e+07 - 11 34 2 0.1430 8.1800e+06 14 16 2 0.1090 1.2300e+07 - 14 15 2 0.1090 1.2300e+07 - 14 48 2 0.1430 8.1800e+06 14 17 2 0.1530 7.1500e+06 + 14 48 2 0.1430 8.1800e+06 + 14 15 2 0.1090 1.2300e+07 17 18 2 0.1090 1.2300e+07 17 19 2 0.1090 1.2300e+07 17 20 2 0.1430 8.1800e+06 - 21 24 2 0.1530 7.1500e+06 21 55 2 0.1430 8.1800e+06 21 23 2 0.1090 1.2300e+07 + 21 24 2 0.1530 7.1500e+06 21 22 2 0.1090 1.2300e+07 - 24 25 2 0.1090 1.2300e+07 24 27 2 0.1430 8.1800e+06 + 24 25 2 0.1090 1.2300e+07 24 26 2 0.1090 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0.0000 5.9200e+00 3 70 73 76 42 1 0.0000 1.2600e+00 3 83 49 52 55 1 0.0000 5.9200e+00 3 77 80 83 49 1 0.0000 1.2600e+00 3 90 56 59 62 1 0.0000 5.9200e+00 3 84 87 90 56 1 0.0000 1.2600e+00 3 - 91 94 97 63 1 0.0000 1.2600e+00 3 97 63 66 69 1 0.0000 5.9200e+00 3 + 91 94 97 63 1 0.0000 1.2600e+00 3 98 70 73 76 1 0.0000 5.9200e+00 3 102 77 80 83 1 0.0000 5.9200e+00 3 106 84 87 90 1 0.0000 5.9200e+00 3 diff --git a/data_paper_examples/four_arm_star_overlapped_monomers.json b/data_paper_examples/four_arm_star_overlapped_monomers.json index c887391..5313cd4 100644 --- a/data_paper_examples/four_arm_star_overlapped_monomers.json +++ b/data_paper_examples/four_arm_star_overlapped_monomers.json @@ -1 +1 @@ -{"topology": {"atoms": [{"atom_id": 1, "atom_type": "HC", "residue_id": 1, "residue_name": "8WDY", "atom_name": "H10", "charge_group_num": 4, "partial_charge": 0.010499999999999999, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 2, "atom_type": "HC", "residue_id": 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{"atom_a": 74, "atom_b": 77, "pair_type": 1}, {"atom_a": 74, "atom_b": 76, "pair_type": 1}, {"atom_a": 80, "atom_b": 84, "pair_type": 1}, {"atom_a": 80, "atom_b": 85, "pair_type": 1}, {"atom_a": 80, "atom_b": 83, "pair_type": 1}, {"atom_a": 81, "atom_b": 84, "pair_type": 1}, {"atom_a": 81, "atom_b": 85, "pair_type": 1}, {"atom_a": 81, "atom_b": 83, "pair_type": 1}, {"atom_a": 89, "atom_b": 92, "pair_type": 1}, {"atom_a": 89, "atom_b": 94, "pair_type": 1}, {"atom_a": 89, "atom_b": 93, "pair_type": 1}, {"atom_a": 90, "atom_b": 93, "pair_type": 1}, {"atom_a": 90, "atom_b": 94, "pair_type": 1}, {"atom_a": 90, "atom_b": 92, "pair_type": 1}], "exclusions": [], "preamble": [";----------------------------TITLE -----------------------------------------------------------------------------------------", "; Pentaerythritol", ";", "; This file was generated at 13:37 on 2024-11-22 by", ";", "; Automatic Topology Builder", ";", "; REVISION 2024-11-20 12:06:25", ";---------------------------------------------------------------------------------------------------------------------------", "; Authors : Martin Stroet, Bertrand Caron, Alpeshkumar K. Malde, Thomas Lee, Alan E. Mark", ";", "; Institute : Molecular Dynamics group,", "; School of Chemistry and Molecular Biosciences (SCMB),", "; The University of Queensland, QLD 4072, Australia", "; URL : https://atb.uq.edu.au", "; Citations : 1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, Nair PC, Oostenbrink C, Mark AE.", "; An Automated force field Topology Builder (ATB) and repository: version 1.0.", "; Journal of Chemical Theory and Computation, 2011, 7, 4026-4037.", "; 2. Stroet M, Caron B, Visscher K, Geerke D, Malde AK, Mark AE.", "; Automated Topology Builder version 3.0: Prediction of solvation free enthalpies in water and hexane.", "; DOI:10.1021/acs.jctc.8b00768", ";", "; Disclaimer :", "; While every effort has been made to ensure the accuracy and validity of parameters provided below", "; the assignment of parameters is being based on an automated procedure combining data provided by a", "; given user as well as calculations performed using third party software. They are provided as a guide.", "; The authors of the ATB cannot guarantee that the parameters are complete or that the parameters provided", "; are appropriate for use in any specific application. Users are advised to treat these parameters with discretion", "; and to perform additional validation tests for their specific application if required. Neither the authors", "; of the ATB or The University of Queensland except any responsibly for how the parameters may be used.", ";", "; Release notes and warnings:", "; (1) The topology is based on a set of atomic coordinates and other data provided by the user after", "; after quantum mechanical optimization of the structure using different levels of theory depending on", "; the nature of the molecule.", "; (2) In some cases the automatic bond, bond angle and dihedral type assignment is ambiguous.", "; In these cases alternative type codes are provided at the end of the line.", "; (3) While bonded parameters are taken where possible from the nominated force field non-standard bond, angle and dihedral", "; type code may be incorporated in cases where an exact match could not be found. These are marked as \"non-standard\"", "; or \"uncertain\" in comments.", "; (4) In some cases it is not possible to assign an appropriate parameter automatically. \"%%\" is used as a place holder", "; for those fields that could not be determined automatically. The parameters in these fields must be assigned manually", "; before the file can be used.", ";---------------------------------------------------------------------------------------------------------------------------", "; Input Structure : 8WDY", "; Output : ALL ATOM topology", ";\tUse in conjunction with the corresponding all atom PDB file.", ";---------------------------------------------------------------------------------------------------------------------------", "; Citing this topology file", "; ATB molid: 39051", "; ATB Topology Hash: 07f0b", ";---------------------------------------------------------------------------------------------------------------------------", "; Final Topology Generation was performed using:", "; A B3LYP/6-31G* optimized geometry.", "; Bonded and van der Waals parameters were taken from the GROMOS 54A7 parameter set.", "; Initial charges were estimated using the ESP method of Merz-Kollman.", "; Final charges and charge groups were generated by method described in the ATB paper.", "; If required, additional bonded parameters were generated from a Hessian matrix calculated at the B3LYP/6-31G* level of theory.", ";---------------------------------------------------------------------------------------------------------------------------", ";", ";"], "moleculetype": {"name": "8WDY", "nrexcl": 3}}, "junctions": []} \ No newline at end of file +{"topology": {"atoms": [{"atom_id": 1, "atom_type": "HC", "residue_id": 1, "residue_name": "8WDY", "atom_name": "H10", "charge_group_num": 4, "partial_charge": 0.010499999999999999, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 2, "atom_type": "HC", "residue_id": 1, "residue_name": "8WDY", "atom_name": "H11", "charge_group_num": 5, "partial_charge": 0.010499999999999999, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 3, "atom_type": "C", "residue_id": 1, "residue_name": "8WDY", "atom_name": "C2", "charge_group_num": 6, "partial_charge": -0.014500000000000002, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 4, "atom_type": "HC", "residue_id": 1, "residue_name": "8WDY", "atom_name": "H2", "charge_group_num": 8, "partial_charge": 0.010499999999999999, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 5, "atom_type": "HC", "residue_id": 1, "residue_name": "8WDY", "atom_name": "H3", "charge_group_num": 9, "partial_charge": 0.010499999999999999, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 6, "atom_type": "HC", "residue_id": 1, "residue_name": "8WDY", "atom_name": "H4", "charge_group_num": 13, "partial_charge": 0.010499999999999999, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 7, "atom_type": "HC", "residue_id": 1, "residue_name": "8WDY", "atom_name": "H5", "charge_group_num": 14, "partial_charge": 0.010499999999999999, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 8, "atom_type": "HC", "residue_id": 1, "residue_name": "8WDY", "atom_name": "H7", "charge_group_num": 18, "partial_charge": 0.010499999999999999, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 9, "atom_type": "HC", "residue_id": 1, "residue_name": "8WDY", "atom_name": "H8", "charge_group_num": 19, "partial_charge": 0.010499999999999999, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 10, "atom_type": "HC", "residue_id": 2, "residue_name": "4Y3B", "atom_name": "H6", "charge_group_num": 4, "partial_charge": 0.0063333333333333375, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 11, "atom_type": "HC", "residue_id": 2, "residue_name": "4Y3B", "atom_name": "H7", "charge_group_num": 5, "partial_charge": 0.0063333333333333375, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 12, "atom_type": "CPos", "residue_id": 2, "residue_name": "4Y3B", "atom_name": "C2", "charge_group_num": 6, "partial_charge": 0.16733333333333333, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 13, "atom_type": "HC", "residue_id": 2, "residue_name": "4Y3B", "atom_name": "H4", "charge_group_num": 7, "partial_charge": 0.036333333333333336, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 14, "atom_type": "HC", "residue_id": 2, "residue_name": "4Y3B", "atom_name": "H5", "charge_group_num": 8, "partial_charge": 0.036333333333333336, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 15, "atom_type": "OE", "residue_id": 2, "residue_name": "4Y3B", "atom_name": "O1", "charge_group_num": 9, "partial_charge": -0.44066666666666665, "mass": 15.9994, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 16, "atom_type": "CPos", "residue_id": 1, "residue_name": "8WDY", "atom_name": "C1", "charge_group_num": 7, "partial_charge": 0.2315, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 17, 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"atom_d": 44, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 1.26, "multiplicity": 3, "constants": []}, {"atom_a": 78, "atom_b": 79, "atom_c": 47, "atom_d": 50, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 79, "atom_b": 47, "atom_c": 50, "atom_d": 51, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 1.26, "multiplicity": 3, "constants": []}, {"atom_a": 86, "atom_b": 54, "atom_c": 57, "atom_d": 58, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 1.26, "multiplicity": 3, "constants": []}, {"atom_a": 85, "atom_b": 86, "atom_c": 54, "atom_d": 57, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 95, "atom_b": 61, "atom_c": 64, "atom_d": 65, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 1.26, "multiplicity": 3, "constants": []}, {"atom_a": 94, "atom_b": 95, "atom_c": 61, "atom_d": 64, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 96, "atom_b": 68, "atom_c": 71, "atom_d": 72, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 1.26, "multiplicity": 3, "constants": []}, {"atom_a": 97, "atom_b": 96, "atom_c": 68, "atom_d": 71, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 102, "atom_b": 101, "atom_c": 75, "atom_d": 78, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 101, "atom_b": 75, "atom_c": 78, "atom_d": 79, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 1.26, "multiplicity": 3, "constants": []}, {"atom_a": 106, "atom_b": 82, "atom_c": 85, "atom_d": 86, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 1.26, "multiplicity": 3, "constants": []}, {"atom_a": 107, "atom_b": 106, "atom_c": 82, "atom_d": 85, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 112, "atom_b": 88, "atom_c": 91, "atom_d": 94, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 88, "atom_b": 91, "atom_c": 94, "atom_d": 95, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 1.26, "multiplicity": 3, "constants": []}], "pairs": [{"atom_a": 1, "atom_b": 16, "pair_type": 1}, {"atom_a": 1, "atom_b": 30, "pair_type": 1}, {"atom_a": 1, "atom_b": 23, "pair_type": 1}, {"atom_a": 2, "atom_b": 23, "pair_type": 1}, {"atom_a": 2, "atom_b": 16, "pair_type": 1}, {"atom_a": 2, "atom_b": 30, "pair_type": 1}, {"atom_a": 4, "atom_b": 30, "pair_type": 1}, {"atom_a": 37, "atom_b": 4, "pair_type": 1}, {"atom_a": 4, "atom_b": 23, "pair_type": 1}, {"atom_a": 37, "atom_b": 5, "pair_type": 1}, {"atom_a": 5, "atom_b": 30, "pair_type": 1}, {"atom_a": 5, "atom_b": 23, "pair_type": 1}, {"atom_a": 6, "atom_b": 30, "pair_type": 1}, {"atom_a": 37, "atom_b": 6, "pair_type": 1}, {"atom_a": 16, "atom_b": 6, "pair_type": 1}, {"atom_a": 7, "atom_b": 30, "pair_type": 1}, {"atom_a": 16, "atom_b": 7, "pair_type": 1}, {"atom_a": 37, "atom_b": 7, "pair_type": 1}, {"atom_a": 16, "atom_b": 8, "pair_type": 1}, {"atom_a": 23, "atom_b": 8, "pair_type": 1}, {"atom_a": 37, "atom_b": 8, "pair_type": 1}, {"atom_a": 37, "atom_b": 9, "pair_type": 1}, {"atom_a": 16, "atom_b": 9, "pair_type": 1}, {"atom_a": 23, "atom_b": 9, "pair_type": 1}, {"atom_a": 10, "atom_b": 13, "pair_type": 1}, {"atom_a": 10, "atom_b": 14, "pair_type": 1}, {"atom_a": 10, "atom_b": 15, "pair_type": 1}, {"atom_a": 11, "atom_b": 13, "pair_type": 1}, {"atom_a": 11, "atom_b": 15, "pair_type": 1}, {"atom_a": 11, "atom_b": 14, "pair_type": 1}, {"atom_a": 17, "atom_b": 21, "pair_type": 1}, {"atom_a": 17, "atom_b": 20, "pair_type": 1}, {"atom_a": 17, "atom_b": 22, "pair_type": 1}, {"atom_a": 18, "atom_b": 20, "pair_type": 1}, {"atom_a": 18, "atom_b": 21, "pair_type": 1}, {"atom_a": 18, "atom_b": 22, "pair_type": 1}, {"atom_a": 24, "atom_b": 28, "pair_type": 1}, {"atom_a": 24, "atom_b": 27, "pair_type": 1}, {"atom_a": 24, "atom_b": 29, "pair_type": 1}, {"atom_a": 25, "atom_b": 29, "pair_type": 1}, {"atom_a": 25, "atom_b": 27, "pair_type": 1}, {"atom_a": 25, "atom_b": 28, "pair_type": 1}, {"atom_a": 31, "atom_b": 36, "pair_type": 1}, {"atom_a": 31, "atom_b": 35, "pair_type": 1}, {"atom_a": 31, "atom_b": 34, "pair_type": 1}, {"atom_a": 32, "atom_b": 35, "pair_type": 1}, {"atom_a": 32, "atom_b": 36, "pair_type": 1}, {"atom_a": 32, "atom_b": 34, "pair_type": 1}, {"atom_a": 38, "atom_b": 41, "pair_type": 1}, {"atom_a": 38, "atom_b": 43, "pair_type": 1}, {"atom_a": 38, "atom_b": 42, "pair_type": 1}, {"atom_a": 39, "atom_b": 43, "pair_type": 1}, {"atom_a": 39, "atom_b": 41, "pair_type": 1}, {"atom_a": 39, "atom_b": 42, "pair_type": 1}, {"atom_a": 45, "atom_b": 49, "pair_type": 1}, {"atom_a": 45, "atom_b": 48, "pair_type": 1}, {"atom_a": 45, "atom_b": 50, "pair_type": 1}, {"atom_a": 46, "atom_b": 48, "pair_type": 1}, {"atom_a": 46, "atom_b": 49, "pair_type": 1}, {"atom_a": 46, "atom_b": 50, "pair_type": 1}, {"atom_a": 52, "atom_b": 57, "pair_type": 1}, {"atom_a": 52, "atom_b": 55, "pair_type": 1}, {"atom_a": 52, "atom_b": 56, "pair_type": 1}, {"atom_a": 53, "atom_b": 55, "pair_type": 1}, {"atom_a": 53, "atom_b": 56, "pair_type": 1}, {"atom_a": 53, "atom_b": 57, "pair_type": 1}, {"atom_a": 59, "atom_b": 62, "pair_type": 1}, {"atom_a": 59, "atom_b": 64, "pair_type": 1}, {"atom_a": 59, "atom_b": 63, "pair_type": 1}, {"atom_a": 60, "atom_b": 63, "pair_type": 1}, {"atom_a": 60, "atom_b": 64, "pair_type": 1}, {"atom_a": 60, "atom_b": 62, "pair_type": 1}, {"atom_a": 66, "atom_b": 69, "pair_type": 1}, {"atom_a": 66, "atom_b": 71, "pair_type": 1}, {"atom_a": 66, "atom_b": 70, "pair_type": 1}, {"atom_a": 67, "atom_b": 69, "pair_type": 1}, {"atom_a": 67, "atom_b": 71, "pair_type": 1}, {"atom_a": 67, "atom_b": 70, "pair_type": 1}, {"atom_a": 73, "atom_b": 78, "pair_type": 1}, {"atom_a": 73, "atom_b": 76, "pair_type": 1}, {"atom_a": 73, "atom_b": 77, "pair_type": 1}, {"atom_a": 74, "atom_b": 78, "pair_type": 1}, {"atom_a": 74, "atom_b": 76, "pair_type": 1}, {"atom_a": 74, "atom_b": 77, "pair_type": 1}, {"atom_a": 80, "atom_b": 85, "pair_type": 1}, {"atom_a": 80, "atom_b": 83, "pair_type": 1}, {"atom_a": 80, "atom_b": 84, "pair_type": 1}, {"atom_a": 81, "atom_b": 84, "pair_type": 1}, {"atom_a": 81, "atom_b": 85, "pair_type": 1}, {"atom_a": 81, "atom_b": 83, "pair_type": 1}, {"atom_a": 89, "atom_b": 94, "pair_type": 1}, {"atom_a": 89, "atom_b": 92, "pair_type": 1}, {"atom_a": 89, "atom_b": 93, "pair_type": 1}, {"atom_a": 90, "atom_b": 94, "pair_type": 1}, {"atom_a": 90, "atom_b": 92, "pair_type": 1}, {"atom_a": 90, "atom_b": 93, "pair_type": 1}], "exclusions": [], "preamble": [";----------------------------TITLE -----------------------------------------------------------------------------------------", "; Pentaerythritol", ";", "; This file was generated at 13:37 on 2024-11-22 by", ";", "; Automatic Topology Builder", ";", "; REVISION 2024-11-20 12:06:25", ";---------------------------------------------------------------------------------------------------------------------------", "; Authors : Martin Stroet, Bertrand Caron, Alpeshkumar K. Malde, Thomas Lee, Alan E. Mark", ";", "; Institute : Molecular Dynamics group,", "; School of Chemistry and Molecular Biosciences (SCMB),", "; The University of Queensland, QLD 4072, Australia", "; URL : https://atb.uq.edu.au", "; Citations : 1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, Nair PC, Oostenbrink C, Mark AE.", "; An Automated force field Topology Builder (ATB) and repository: version 1.0.", "; Journal of Chemical Theory and Computation, 2011, 7, 4026-4037.", "; 2. Stroet M, Caron B, Visscher K, Geerke D, Malde AK, Mark AE.", "; Automated Topology Builder version 3.0: Prediction of solvation free enthalpies in water and hexane.", "; DOI:10.1021/acs.jctc.8b00768", ";", "; Disclaimer :", "; While every effort has been made to ensure the accuracy and validity of parameters provided below", "; the assignment of parameters is being based on an automated procedure combining data provided by a", "; given user as well as calculations performed using third party software. They are provided as a guide.", "; The authors of the ATB cannot guarantee that the parameters are complete or that the parameters provided", "; are appropriate for use in any specific application. Users are advised to treat these parameters with discretion", "; and to perform additional validation tests for their specific application if required. Neither the authors", "; of the ATB or The University of Queensland except any responsibly for how the parameters may be used.", ";", "; Release notes and warnings:", "; (1) The topology is based on a set of atomic coordinates and other data provided by the user after", "; after quantum mechanical optimization of the structure using different levels of theory depending on", "; the nature of the molecule.", "; (2) In some cases the automatic bond, bond angle and dihedral type assignment is ambiguous.", "; In these cases alternative type codes are provided at the end of the line.", "; (3) While bonded parameters are taken where possible from the nominated force field non-standard bond, angle and dihedral", "; type code may be incorporated in cases where an exact match could not be found. These are marked as \"non-standard\"", "; or \"uncertain\" in comments.", "; (4) In some cases it is not possible to assign an appropriate parameter automatically. \"%%\" is used as a place holder", "; for those fields that could not be determined automatically. The parameters in these fields must be assigned manually", "; before the file can be used.", ";---------------------------------------------------------------------------------------------------------------------------", "; Input Structure : 8WDY", "; Output : ALL ATOM topology", ";\tUse in conjunction with the corresponding all atom PDB file.", ";---------------------------------------------------------------------------------------------------------------------------", "; Citing this topology file", "; ATB molid: 39051", "; ATB Topology Hash: 07f0b", ";---------------------------------------------------------------------------------------------------------------------------", "; Final Topology Generation was performed using:", "; A B3LYP/6-31G* optimized geometry.", "; Bonded and van der Waals parameters were taken from the GROMOS 54A7 parameter set.", "; Initial charges were estimated using the ESP method of Merz-Kollman.", "; Final charges and charge groups were generated by method described in the ATB paper.", "; If required, additional bonded parameters were generated from a Hessian matrix calculated at the B3LYP/6-31G* level of theory.", ";---------------------------------------------------------------------------------------------------------------------------", ";", ";"], "moleculetype": {"name": "8WDY", "nrexcl": 3}}, "junctions": []} \ No newline at end of file diff --git a/data_paper_examples/four_arm_star_overlapped_monomers.png b/data_paper_examples/four_arm_star_overlapped_monomers.png index 162a456..18c3cec 100644 Binary files a/data_paper_examples/four_arm_star_overlapped_monomers.png and b/data_paper_examples/four_arm_star_overlapped_monomers.png differ diff --git a/data_paper_examples/pei_linear_polymer.itp b/data_paper_examples/pei_linear_polymer.itp index 354d20d..09f46bf 100644 --- a/data_paper_examples/pei_linear_polymer.itp +++ b/data_paper_examples/pei_linear_polymer.itp @@ -212,8 +212,8 @@ LHCU 3 [ bonds ] 1 2 2 0.1530 7.1500e+06 2 3 2 0.1470 8.7100e+06 - 3 5 2 0.1470 8.7100e+06 3 4 2 0.1020 1.7782e+07 + 3 5 2 0.1470 8.7100e+06 5 6 2 0.1530 7.1500e+06 6 7 2 0.1470 8.7100e+06 7 9 2 0.1500 8.7100e+06 @@ -223,11 +223,11 @@ LHCU 3 10 11 2 0.1020 1.7782e+07 12 13 2 0.1530 7.1500e+06 13 14 2 0.1470 8.7100e+06 + 14 16 2 0.1500 8.7100e+06 14 15 2 0.1020 1.7782e+07 - 14 16 2 0.1500 7.1500e+06 16 17 2 0.1470 8.7100e+06 - 17 18 2 0.1020 1.7782e+07 17 19 2 0.1470 8.7100e+06 + 17 18 2 0.1020 1.7782e+07 19 20 2 0.1530 7.1500e+06 20 21 2 0.1470 8.7100e+06 21 22 2 0.1020 1.7782e+07 @@ -237,11 +237,11 @@ LHCU 3 24 26 2 0.1470 8.7100e+06 26 27 2 0.1530 7.1500e+06 27 28 2 0.1470 8.7100e+06 - 28 30 2 0.1500 8.7100e+06 28 29 2 0.1020 1.7782e+07 + 28 30 2 0.1500 8.7100e+06 30 31 2 0.1470 8.7100e+06 - 31 33 2 0.1470 8.7100e+06 31 32 2 0.1020 1.7782e+07 + 31 33 2 0.1470 8.7100e+06 33 34 2 0.1530 7.1500e+06 34 35 2 0.1470 8.7100e+06 35 37 2 0.1500 8.7100e+06 @@ -251,11 +251,11 @@ LHCU 3 38 40 2 0.1470 8.7100e+06 40 41 2 0.1530 7.1500e+06 41 42 2 0.1470 8.7100e+06 - 42 44 2 0.1500 8.7100e+06 42 43 2 0.1020 1.7782e+07 + 42 44 2 0.1500 8.7100e+06 44 45 2 0.1470 8.7100e+06 - 45 47 2 0.1470 8.7100e+06 45 46 2 0.1020 1.7782e+07 + 45 47 2 0.1470 8.7100e+06 47 48 2 0.1530 7.1500e+06 48 49 2 0.1470 8.7100e+06 49 51 2 0.1500 8.7100e+06 @@ -265,11 +265,11 @@ LHCU 3 52 54 2 0.1470 8.7100e+06 54 55 2 0.1530 7.1500e+06 55 56 2 0.1470 8.7100e+06 - 56 57 2 0.1020 1.7782e+07 56 58 2 0.1500 8.7100e+06 + 56 57 2 0.1020 1.7782e+07 58 59 2 0.1470 8.7100e+06 - 59 61 2 0.1470 8.7100e+06 59 60 2 0.1020 1.7782e+07 + 59 61 2 0.1470 8.7100e+06 61 62 2 0.1530 7.1500e+06 62 63 2 0.1470 8.7100e+06 63 65 2 0.1500 8.7100e+06 @@ -287,74 +287,74 @@ LHCU 3 75 76 2 0.1530 7.1500e+06 76 77 2 0.1470 8.7100e+06 77 78 2 0.1020 1.7782e+07 - 77 79 2 0.1500 7.1500e+06 + 77 79 2 0.1500 8.7100e+06 79 80 2 0.1470 8.7100e+06 80 81 2 0.1020 1.7782e+07 80 82 2 0.1470 8.7100e+06 82 83 2 0.1530 7.1500e+06 83 84 2 0.1470 8.7100e+06 - 84 86 2 0.1500 7.1500e+06 + 84 86 2 0.1500 8.7100e+06 84 85 2 0.1020 1.7782e+07 86 87 2 0.1470 8.7100e+06 87 89 2 0.1470 8.7100e+06 87 88 2 0.1020 1.7782e+07 89 90 2 0.1530 7.1500e+06 90 91 2 0.1470 8.7100e+06 - 91 93 2 0.1500 7.1500e+06 91 92 2 0.1020 1.7782e+07 + 91 93 2 0.1500 8.7100e+06 93 94 2 0.1470 8.7100e+06 - 94 96 2 0.1470 8.7100e+06 94 95 2 0.1020 1.7782e+07 + 94 96 2 0.1470 8.7100e+06 96 97 2 0.1530 7.1500e+06 97 98 2 0.1470 8.7100e+06 - 98 100 2 0.1500 7.1500e+06 98 99 2 0.1020 1.7782e+07 + 98 100 2 0.1500 8.7100e+06 100 101 2 0.1470 8.7100e+06 101 103 2 0.1470 8.7100e+06 101 102 2 0.1020 1.7782e+07 103 104 2 0.1530 7.1500e+06 104 105 2 0.1470 8.7100e+06 105 106 2 0.1020 1.7782e+07 - 105 107 2 0.1500 7.1500e+06 + 105 107 2 0.1500 8.7100e+06 107 108 2 0.1470 8.7100e+06 108 110 2 0.1470 8.7100e+06 108 109 2 0.1020 1.7782e+07 110 111 2 0.1530 7.1500e+06 111 112 2 0.1470 8.7100e+06 - 112 113 2 0.1020 1.7782e+07 112 114 2 0.1500 8.7100e+06 + 112 113 2 0.1020 1.7782e+07 114 115 2 0.1470 8.7100e+06 - 115 116 2 0.1020 1.7782e+07 115 117 2 0.1470 8.7100e+06 + 115 116 2 0.1020 1.7782e+07 117 118 2 0.1530 7.1500e+06 118 119 2 0.1470 8.7100e+06 119 120 2 0.1020 1.7782e+07 - 119 121 2 0.1500 7.1500e+06 + 119 121 2 0.1500 8.7100e+06 121 122 2 0.1470 8.7100e+06 - 122 124 2 0.1470 8.7100e+06 122 123 2 0.1020 1.7782e+07 + 122 124 2 0.1470 8.7100e+06 124 125 2 0.1530 7.1500e+06 125 126 2 0.1470 8.7100e+06 - 126 128 2 0.1500 7.1500e+06 + 126 128 2 0.1500 8.7100e+06 126 127 2 0.1020 1.7782e+07 128 129 2 0.1470 8.7100e+06 129 130 2 0.1020 1.7782e+07 129 131 2 0.1470 8.7100e+06 131 132 2 0.1530 7.1500e+06 132 133 2 0.1470 8.7100e+06 - 133 135 2 0.1500 7.1500e+06 + 133 135 2 0.1500 8.7100e+06 133 134 2 0.1020 1.7782e+07 135 136 2 0.1470 8.7100e+06 - 136 137 2 0.1020 1.7782e+07 136 138 2 0.1470 8.7100e+06 + 136 137 2 0.1020 1.7782e+07 138 139 2 0.1530 7.1500e+06 139 140 2 0.1470 8.7100e+06 - 140 141 2 0.1020 1.7782e+07 140 142 2 0.1470 8.7100e+06 + 140 141 2 0.1020 1.7782e+07 [ pairs ] - 1 5 1 1 4 1 + 1 5 1 2 6 1 3 7 1 4 6 1 @@ -439,8 +439,8 @@ LHCU 3 [ angles ] 1 2 3 2 111.0000 5.3000e+02 - 2 3 4 2 109.5000 4.2500e+02 2 3 5 2 116.0000 6.2000e+02 + 2 3 4 2 109.5000 4.2500e+02 4 3 5 2 109.5000 4.2500e+02 3 5 6 2 111.0000 5.3000e+02 5 6 7 2 111.0000 5.3000e+02 @@ -448,8 +448,8 @@ LHCU 3 6 7 9 2 116.0000 6.2000e+02 7 9 10 2 111.0000 5.3000e+02 8 7 9 2 109.5000 4.2500e+02 - 9 10 12 2 116.0000 6.2000e+02 9 10 11 2 109.5000 4.2500e+02 + 9 10 12 2 116.0000 6.2000e+02 11 10 12 2 109.5000 4.2500e+02 10 12 13 2 111.0000 5.3000e+02 12 13 14 2 111.0000 5.3000e+02 @@ -457,31 +457,31 @@ LHCU 3 13 14 15 2 109.5000 4.2500e+02 15 14 16 2 109.5000 4.2500e+02 14 16 17 2 111.0000 5.3000e+02 - 16 17 19 2 116.0000 6.2000e+02 16 17 18 2 109.5000 4.2500e+02 - 18 17 19 2 109.5000 4.2500e+02 + 16 17 19 2 116.0000 6.2000e+02 17 19 20 2 111.0000 5.3000e+02 + 18 17 19 2 109.5000 4.2500e+02 19 20 21 2 111.0000 5.3000e+02 - 20 21 23 2 116.0000 6.2000e+02 20 21 22 2 109.5000 4.2500e+02 + 20 21 23 2 116.0000 6.2000e+02 22 21 23 2 109.5000 4.2500e+02 21 23 24 2 111.0000 5.3000e+02 - 23 24 26 2 116.0000 6.2000e+02 23 24 25 2 109.5000 4.2500e+02 + 23 24 26 2 116.0000 6.2000e+02 25 24 26 2 109.5000 4.2500e+02 24 26 27 2 111.0000 5.3000e+02 26 27 28 2 111.0000 5.3000e+02 27 28 30 2 116.0000 6.2000e+02 27 28 29 2 109.5000 4.2500e+02 - 28 30 31 2 111.0000 5.3000e+02 29 28 30 2 109.5000 4.2500e+02 - 30 31 33 2 116.0000 6.2000e+02 + 28 30 31 2 111.0000 5.3000e+02 30 31 32 2 109.5000 4.2500e+02 + 30 31 33 2 116.0000 6.2000e+02 32 31 33 2 109.5000 4.2500e+02 31 33 34 2 111.0000 5.3000e+02 33 34 35 2 111.0000 5.3000e+02 - 34 35 36 2 109.5000 4.2500e+02 34 35 37 2 116.0000 6.2000e+02 + 34 35 36 2 109.5000 4.2500e+02 36 35 37 2 109.5000 4.2500e+02 35 37 38 2 111.0000 5.3000e+02 37 38 39 2 109.5000 4.2500e+02 @@ -493,15 +493,15 @@ LHCU 3 41 42 43 2 109.5000 4.2500e+02 43 42 44 2 109.5000 4.2500e+02 42 44 45 2 111.0000 5.3000e+02 - 44 45 46 2 109.5000 4.2500e+02 44 45 47 2 116.0000 6.2000e+02 - 45 47 48 2 111.0000 5.3000e+02 + 44 45 46 2 109.5000 4.2500e+02 46 45 47 2 109.5000 4.2500e+02 + 45 47 48 2 111.0000 5.3000e+02 47 48 49 2 111.0000 5.3000e+02 - 48 49 50 2 109.5000 4.2500e+02 48 49 51 2 116.0000 6.2000e+02 - 50 49 51 2 109.5000 4.2500e+02 + 48 49 50 2 109.5000 4.2500e+02 49 51 52 2 111.0000 5.3000e+02 + 50 49 51 2 109.5000 4.2500e+02 51 52 53 2 109.5000 4.2500e+02 51 52 54 2 116.0000 6.2000e+02 53 52 54 2 109.5000 4.2500e+02 @@ -509,19 +509,19 @@ LHCU 3 54 55 56 2 111.0000 5.3000e+02 55 56 57 2 109.5000 4.2500e+02 55 56 58 2 116.0000 6.2000e+02 - 57 56 58 2 109.5000 4.2500e+02 56 58 59 2 111.0000 5.3000e+02 + 57 56 58 2 109.5000 4.2500e+02 58 59 61 2 116.0000 6.2000e+02 58 59 60 2 109.5000 4.2500e+02 - 59 61 62 2 111.0000 5.3000e+02 60 59 61 2 109.5000 4.2500e+02 + 59 61 62 2 111.0000 5.3000e+02 61 62 63 2 111.0000 5.3000e+02 - 62 63 64 2 109.5000 4.2500e+02 62 63 65 2 116.0000 6.2000e+02 + 62 63 64 2 109.5000 4.2500e+02 64 63 65 2 109.5000 4.2500e+02 63 65 66 2 111.0000 5.3000e+02 - 65 66 68 2 116.0000 6.2000e+02 65 66 67 2 109.5000 4.2500e+02 + 65 66 68 2 116.0000 6.2000e+02 67 66 68 2 109.5000 4.2500e+02 66 68 69 2 111.0000 5.3000e+02 68 69 70 2 111.0000 5.3000e+02 @@ -543,28 +543,28 @@ LHCU 3 81 80 82 2 109.5000 4.2500e+02 80 82 83 2 111.0000 5.3000e+02 82 83 84 2 111.0000 5.3000e+02 - 83 84 86 2 116.0000 6.2000e+02 83 84 85 2 109.5000 4.2500e+02 - 84 86 87 2 111.0000 5.3000e+02 + 83 84 86 2 116.0000 6.2000e+02 85 84 86 2 109.5000 4.2500e+02 - 86 87 89 2 116.0000 6.2000e+02 + 84 86 87 2 111.0000 5.3000e+02 86 87 88 2 109.5000 4.2500e+02 + 86 87 89 2 116.0000 6.2000e+02 88 87 89 2 109.5000 4.2500e+02 87 89 90 2 111.0000 5.3000e+02 89 90 91 2 111.0000 5.3000e+02 90 91 92 2 109.5000 4.2500e+02 90 91 93 2 116.0000 6.2000e+02 - 91 93 94 2 111.0000 5.3000e+02 92 91 93 2 109.5000 4.2500e+02 - 93 94 95 2 109.5000 4.2500e+02 + 91 93 94 2 111.0000 5.3000e+02 93 94 96 2 116.0000 6.2000e+02 - 94 96 97 2 111.0000 5.3000e+02 + 93 94 95 2 109.5000 4.2500e+02 95 94 96 2 109.5000 4.2500e+02 + 94 96 97 2 111.0000 5.3000e+02 96 97 98 2 111.0000 5.3000e+02 97 98 99 2 109.5000 4.2500e+02 97 98 100 2 116.0000 6.2000e+02 - 98 100 101 2 111.0000 5.3000e+02 99 98 100 2 109.5000 4.2500e+02 + 98 100 101 2 111.0000 5.3000e+02 100 101 102 2 109.5000 4.2500e+02 100 101 103 2 116.0000 6.2000e+02 102 101 103 2 109.5000 4.2500e+02 @@ -574,13 +574,13 @@ LHCU 3 104 105 107 2 116.0000 6.2000e+02 106 105 107 2 109.5000 4.2500e+02 105 107 108 2 111.0000 5.3000e+02 - 107 108 109 2 109.5000 4.2500e+02 107 108 110 2 116.0000 6.2000e+02 + 107 108 109 2 109.5000 4.2500e+02 109 108 110 2 109.5000 4.2500e+02 108 110 111 2 111.0000 5.3000e+02 110 111 112 2 111.0000 5.3000e+02 - 111 112 114 2 116.0000 6.2000e+02 111 112 113 2 109.5000 4.2500e+02 + 111 112 114 2 116.0000 6.2000e+02 113 112 114 2 109.5000 4.2500e+02 112 114 115 2 111.0000 5.3000e+02 114 115 116 2 109.5000 4.2500e+02 @@ -592,13 +592,13 @@ LHCU 3 118 119 121 2 116.0000 6.2000e+02 120 119 121 2 109.5000 4.2500e+02 119 121 122 2 111.0000 5.3000e+02 - 121 122 124 2 116.0000 6.2000e+02 121 122 123 2 109.5000 4.2500e+02 - 122 124 125 2 111.0000 5.3000e+02 + 121 122 124 2 116.0000 6.2000e+02 123 122 124 2 109.5000 4.2500e+02 + 122 124 125 2 111.0000 5.3000e+02 124 125 126 2 111.0000 5.3000e+02 - 125 126 127 2 109.5000 4.2500e+02 125 126 128 2 116.0000 6.2000e+02 + 125 126 127 2 109.5000 4.2500e+02 126 128 129 2 111.0000 5.3000e+02 127 126 128 2 109.5000 4.2500e+02 128 129 131 2 116.0000 6.2000e+02 @@ -610,8 +610,8 @@ LHCU 3 132 133 134 2 109.5000 4.2500e+02 133 135 136 2 111.0000 5.3000e+02 134 133 135 2 109.5000 4.2500e+02 - 135 136 138 2 116.0000 6.2000e+02 135 136 137 2 109.5000 4.2500e+02 + 135 136 138 2 116.0000 6.2000e+02 137 136 138 2 109.5000 4.2500e+02 136 138 139 2 111.0000 5.3000e+02 138 139 140 2 111.0000 5.3000e+02 diff --git a/data_paper_examples/pei_linear_polymer.json b/data_paper_examples/pei_linear_polymer.json index 91b6390..b62e06c 100644 --- a/data_paper_examples/pei_linear_polymer.json +++ 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"atom_b": 7, "pair_type": 1}, {"atom_a": 9, "atom_b": 13, "pair_type": 1}, {"atom_a": 10, "atom_b": 15, "pair_type": 1}, {"atom_a": 11, "atom_b": 13, "pair_type": 1}, {"atom_a": 12, "atom_b": 14, "pair_type": 1}, {"atom_a": 16, "atom_b": 20, "pair_type": 1}, {"atom_a": 17, "atom_b": 22, "pair_type": 1}, {"atom_a": 18, "atom_b": 20, "pair_type": 1}, {"atom_a": 19, "atom_b": 21, "pair_type": 1}, {"atom_a": 23, "atom_b": 27, "pair_type": 1}, {"atom_a": 24, "atom_b": 29, "pair_type": 1}, {"atom_a": 25, "atom_b": 27, "pair_type": 1}, {"atom_a": 26, "atom_b": 28, "pair_type": 1}, {"atom_a": 30, "atom_b": 34, "pair_type": 1}, {"atom_a": 31, "atom_b": 36, "pair_type": 1}, {"atom_a": 32, "atom_b": 34, "pair_type": 1}, {"atom_a": 33, "atom_b": 35, "pair_type": 1}, {"atom_a": 37, "atom_b": 41, "pair_type": 1}, {"atom_a": 38, "atom_b": 43, "pair_type": 1}, {"atom_a": 39, "atom_b": 41, "pair_type": 1}, {"atom_a": 40, "atom_b": 42, "pair_type": 1}, {"atom_a": 44, "atom_b": 48, "pair_type": 1}, {"atom_a": 45, "atom_b": 50, "pair_type": 1}, {"atom_a": 46, "atom_b": 48, "pair_type": 1}, {"atom_a": 47, "atom_b": 49, "pair_type": 1}, {"atom_a": 51, "atom_b": 55, "pair_type": 1}, {"atom_a": 52, "atom_b": 57, "pair_type": 1}, {"atom_a": 53, "atom_b": 55, "pair_type": 1}, {"atom_a": 54, "atom_b": 56, "pair_type": 1}, {"atom_a": 58, "atom_b": 62, "pair_type": 1}, {"atom_a": 59, "atom_b": 64, "pair_type": 1}, {"atom_a": 60, "atom_b": 62, "pair_type": 1}, {"atom_a": 61, "atom_b": 63, "pair_type": 1}, {"atom_a": 65, "atom_b": 69, "pair_type": 1}, {"atom_a": 66, "atom_b": 71, "pair_type": 1}, {"atom_a": 67, "atom_b": 69, "pair_type": 1}, {"atom_a": 68, "atom_b": 70, "pair_type": 1}, {"atom_a": 72, "atom_b": 76, "pair_type": 1}, {"atom_a": 73, "atom_b": 78, "pair_type": 1}, {"atom_a": 74, "atom_b": 76, "pair_type": 1}, {"atom_a": 75, "atom_b": 77, "pair_type": 1}, {"atom_a": 79, "atom_b": 83, "pair_type": 1}, {"atom_a": 80, "atom_b": 85, "pair_type": 1}, {"atom_a": 81, "atom_b": 83, "pair_type": 1}, {"atom_a": 82, "atom_b": 84, "pair_type": 1}, {"atom_a": 86, "atom_b": 90, "pair_type": 1}, {"atom_a": 87, "atom_b": 92, "pair_type": 1}, {"atom_a": 88, "atom_b": 90, "pair_type": 1}, {"atom_a": 89, "atom_b": 91, "pair_type": 1}, {"atom_a": 93, "atom_b": 97, "pair_type": 1}, {"atom_a": 94, "atom_b": 99, "pair_type": 1}, {"atom_a": 95, "atom_b": 97, "pair_type": 1}, {"atom_a": 96, "atom_b": 98, "pair_type": 1}, {"atom_a": 100, "atom_b": 104, "pair_type": 1}, {"atom_a": 101, "atom_b": 106, "pair_type": 1}, {"atom_a": 102, "atom_b": 104, "pair_type": 1}, {"atom_a": 103, "atom_b": 105, "pair_type": 1}, {"atom_a": 107, "atom_b": 111, "pair_type": 1}, {"atom_a": 108, "atom_b": 113, "pair_type": 1}, {"atom_a": 109, "atom_b": 111, "pair_type": 1}, {"atom_a": 110, "atom_b": 112, "pair_type": 1}, {"atom_a": 114, "atom_b": 118, "pair_type": 1}, {"atom_a": 115, "atom_b": 120, "pair_type": 1}, {"atom_a": 116, "atom_b": 118, "pair_type": 1}, {"atom_a": 117, "atom_b": 119, "pair_type": 1}, {"atom_a": 121, "atom_b": 125, "pair_type": 1}, {"atom_a": 122, "atom_b": 127, "pair_type": 1}, {"atom_a": 123, "atom_b": 125, "pair_type": 1}, {"atom_a": 124, "atom_b": 126, "pair_type": 1}, {"atom_a": 128, "atom_b": 132, "pair_type": 1}, {"atom_a": 129, "atom_b": 133, "pair_type": 1}, {"atom_a": 130, "atom_b": 132, "pair_type": 1}, {"atom_a": 131, "atom_b": 134, "pair_type": 1}, {"atom_a": 137, "atom_b": 141, "pair_type": 1}, {"atom_a": 138, "atom_b": 142, "pair_type": 1}, {"atom_a": 139, "atom_b": 141, "pair_type": 1}, {"atom_a": 140, "atom_b": 144, "pair_type": 1}, {"atom_a": 140, "atom_b": 143, "pair_type": 1}], "exclusions": [], "preamble": [";----------------------------TITLE -----------------------------------------------------------------------------------------", "; None", ";", "; This file was generated at 14:05 on 2024-12-13 by", ";", "; Automatic Topology Builder", ";", "; REVISION 2024-11-20 12:06:25", ";---------------------------------------------------------------------------------------------------------------------------", "; Authors : Martin Stroet, Bertrand Caron, Alpeshkumar K. Malde, Thomas Lee, Alan E. Mark", ";", "; Institute : Molecular Dynamics group,", "; School of Chemistry and Molecular Biosciences (SCMB),", "; The University of Queensland, QLD 4072, Australia", "; URL : https://atb.uq.edu.au", "; Citations : 1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, Nair PC, Oostenbrink C, Mark AE.", "; An Automated force field Topology Builder (ATB) and repository: version 1.0.", "; Journal of Chemical Theory and Computation, 2011, 7, 4026-4037.", "; 2. Stroet M, Caron B, Visscher K, Geerke D, Malde AK, Mark AE.", "; Automated Topology Builder version 3.0: Prediction of solvation free enthalpies in water and hexane.", "; DOI:10.1021/acs.jctc.8b00768", ";", "; Disclaimer :", "; While every effort has been made to ensure the accuracy and validity of parameters provided below", "; the assignment of parameters is being based on an automated procedure combining data provided by a", "; given user as well as calculations performed using third party software. They are provided as a guide.", "; The authors of the ATB cannot guarantee that the parameters are complete or that the parameters provided", "; are appropriate for use in any specific application. Users are advised to treat these parameters with discretion", "; and to perform additional validation tests for their specific application if required. Neither the authors", "; of the ATB or The University of Queensland except any responsibly for how the parameters may be used.", ";", "; Release notes and warnings:", "; (1) The topology is based on a set of atomic coordinates and other data provided by the user after", "; after quantum mechanical optimization of the structure using different levels of theory depending on", "; the nature of the molecule.", "; (2) In some cases the automatic bond, bond angle and dihedral type assignment is ambiguous.", "; In these cases alternative type codes are provided at the end of the line.", "; (3) While bonded parameters are taken where possible from the nominated force field non-standard bond, angle and dihedral", "; type code may be incorporated in cases where an exact match could not be found. These are marked as \"non-standard\"", "; or \"uncertain\" in comments.", "; (4) In some cases it is not possible to assign an appropriate parameter automatically. \"%%\" is used as a place holder", "; for those fields that could not be determined automatically. The parameters in these fields must be assigned manually", "; before the file can be used.", ";---------------------------------------------------------------------------------------------------------------------------", "; Input Structure : LHCU", "; Output : UNITED ATOM topology", ";\tUse in conjunction with the corresponding united atom PDB file.", ";---------------------------------------------------------------------------------------------------------------------------", "; Citing this topology file", "; ATB molid: 1707355", "; ATB Topology Hash: f968d", ";---------------------------------------------------------------------------------------------------------------------------", "; Final Topology Generation was performed using:", "; A B3LYP/6-31G* optimized geometry.", "; Bonded and van der Waals parameters were taken from the GROMOS 54A7 parameter set.", "; Initial charges were estimated using the ESP method of Merz-Kollman.", "; Final charges and charge groups were generated by method described in the ATB paper.", "; If required, additional bonded parameters were generated from a Hessian matrix calculated at the B3LYP/6-31G* level of theory.", ";---------------------------------------------------------------------------------------------------------------------------", ";", ";"], "moleculetype": {"name": "LHCU", "nrexcl": 3}}, "junctions": [{"name": "to", "monomer_atom": "C51", "residue_atom": "C62"}, {"name": "from", "monomer_atom": "N7", "residue_atom": "C6"}]} \ No newline at end of file +{"topology": {"atoms": [{"atom_id": 1, "atom_type": "CH3", "residue_id": 1, "residue_name": "LHCU", "atom_name": "C62", "charge_group_num": 1, "partial_charge": 0.013437500000000005, "mass": 15.035, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 2, "atom_type": "CH2", "residue_id": 1, "residue_name": "LHCU", "atom_name": "C51", "charge_group_num": 2, "partial_charge": 0.2134375, "mass": 14.027, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 3, "atom_type": "NOpt", "residue_id": 1, "residue_name": "LHCU", "atom_name": "N71", "charge_group_num": 3, "partial_charge": -0.6855625, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 4, "atom_type": "HS14", "residue_id": 1, "residue_name": "LHCU", "atom_name": "H72", "charge_group_num": 4, "partial_charge": 0.30443749999999997, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 5, "atom_type": "CH2", "residue_id": 1, "residue_name": "LHCU", "atom_name": "C61", "charge_group_num": 5, "partial_charge": 0.2104375, "mass": 14.027, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 6, "atom_type": "CH2", "residue_id": 1, "residue_name": "LHCU", "atom_name": "C5", "charge_group_num": 6, "partial_charge": 0.2254375, "mass": 14.027, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 7, "atom_type": "HS14", "residue_id": 1, "residue_name": "LHCU", "atom_name": "H21", "charge_group_num": 8, "partial_charge": 0.3184375, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 8, "atom_type": "NOpt", "residue_id": 1, "residue_name": "LHCU", "atom_name": "N7", "charge_group_num": 7, "partial_charge": -0.6985625, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 9, "atom_type": "CH2", "residue_id": 2, "residue_name": "LHCU", "atom_name": "C51", "charge_group_num": 2, "partial_charge": 0.22753333333333334, "mass": 14.027, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 10, "atom_type": "NOpt", "residue_id": 2, "residue_name": "LHCU", "atom_name": "N71", "charge_group_num": 3, "partial_charge": -0.6714666666666667, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 11, "atom_type": "HS14", "residue_id": 2, "residue_name": "LHCU", "atom_name": "H72", "charge_group_num": 4, "partial_charge": 0.31853333333333333, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 12, "atom_type": "CH2", "residue_id": 2, "residue_name": "LHCU", "atom_name": "C61", "charge_group_num": 5, "partial_charge": 0.22453333333333333, "mass": 14.027, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 13, "atom_type": "CH2", "residue_id": 2, "residue_name": "LHCU", "atom_name": "C5", "charge_group_num": 6, "partial_charge": 0.23953333333333335, "mass": 14.027, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 14, "atom_type": "HS14", "residue_id": 2, "residue_name": "LHCU", "atom_name": "H21", "charge_group_num": 8, "partial_charge": 0.33253333333333335, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 15, "atom_type": "NOpt", "residue_id": 2, "residue_name": "LHCU", "atom_name": "N7", "charge_group_num": 7, "partial_charge": -0.6844666666666667, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 16, "atom_type": "CH2", "residue_id": 3, "residue_name": "LHCU", "atom_name": "C51", "charge_group_num": 2, "partial_charge": 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"dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 93, "atom_b": 94, "atom_c": 96, "atom_d": 97, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 94, "atom_b": 96, "atom_c": 97, "atom_d": 99, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 96, "atom_b": 97, "atom_c": 99, "atom_d": 100, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 99, "atom_b": 100, "atom_c": 101, "atom_d": 103, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 100, "atom_b": 101, "atom_c": 103, "atom_d": 104, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 101, "atom_b": 103, "atom_c": 104, "atom_d": 106, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 103, "atom_b": 104, "atom_c": 106, "atom_d": 107, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 106, "atom_b": 107, "atom_c": 108, "atom_d": 110, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 107, "atom_b": 108, "atom_c": 110, "atom_d": 111, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 108, "atom_b": 110, "atom_c": 111, "atom_d": 113, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 110, "atom_b": 111, "atom_c": 113, "atom_d": 114, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 113, "atom_b": 114, "atom_c": 115, "atom_d": 117, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 114, "atom_b": 115, "atom_c": 117, "atom_d": 118, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 115, "atom_b": 117, "atom_c": 118, "atom_d": 120, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 117, "atom_b": 118, "atom_c": 120, "atom_d": 121, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 120, "atom_b": 121, "atom_c": 122, "atom_d": 124, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 121, "atom_b": 122, "atom_c": 124, "atom_d": 125, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 122, "atom_b": 124, "atom_c": 125, "atom_d": 127, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 124, "atom_b": 125, "atom_c": 127, "atom_d": 128, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 127, "atom_b": 128, "atom_c": 129, "atom_d": 131, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 128, "atom_b": 129, "atom_c": 131, "atom_d": 132, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 129, "atom_b": 131, "atom_c": 132, "atom_d": 133, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 131, "atom_b": 132, "atom_c": 133, "atom_d": 137, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 133, "atom_b": 137, "atom_c": 138, "atom_d": 140, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 137, "atom_b": 138, "atom_c": 140, "atom_d": 141, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 138, "atom_b": 140, "atom_c": 141, "atom_d": 142, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 140, "atom_b": 141, "atom_c": 142, "atom_d": 144, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}], "pairs": [{"atom_a": 1, "atom_b": 4, "pair_type": 1}, {"atom_a": 1, "atom_b": 5, "pair_type": 1}, {"atom_a": 2, "atom_b": 6, "pair_type": 1}, {"atom_a": 3, "atom_b": 8, "pair_type": 1}, {"atom_a": 4, "atom_b": 6, "pair_type": 1}, {"atom_a": 5, "atom_b": 7, "pair_type": 1}, {"atom_a": 9, "atom_b": 13, "pair_type": 1}, {"atom_a": 10, "atom_b": 15, "pair_type": 1}, {"atom_a": 11, "atom_b": 13, "pair_type": 1}, {"atom_a": 12, "atom_b": 14, "pair_type": 1}, {"atom_a": 16, "atom_b": 20, "pair_type": 1}, {"atom_a": 17, "atom_b": 22, "pair_type": 1}, {"atom_a": 18, "atom_b": 20, "pair_type": 1}, {"atom_a": 19, "atom_b": 21, "pair_type": 1}, {"atom_a": 23, "atom_b": 27, "pair_type": 1}, {"atom_a": 24, "atom_b": 29, "pair_type": 1}, {"atom_a": 25, "atom_b": 27, "pair_type": 1}, {"atom_a": 26, "atom_b": 28, "pair_type": 1}, {"atom_a": 30, "atom_b": 34, "pair_type": 1}, {"atom_a": 31, "atom_b": 36, "pair_type": 1}, {"atom_a": 32, "atom_b": 34, "pair_type": 1}, {"atom_a": 33, "atom_b": 35, "pair_type": 1}, {"atom_a": 37, "atom_b": 41, "pair_type": 1}, {"atom_a": 38, "atom_b": 43, "pair_type": 1}, {"atom_a": 39, "atom_b": 41, "pair_type": 1}, {"atom_a": 40, "atom_b": 42, "pair_type": 1}, {"atom_a": 44, "atom_b": 48, "pair_type": 1}, {"atom_a": 45, "atom_b": 50, "pair_type": 1}, {"atom_a": 46, "atom_b": 48, "pair_type": 1}, {"atom_a": 47, "atom_b": 49, "pair_type": 1}, {"atom_a": 51, "atom_b": 55, "pair_type": 1}, {"atom_a": 52, "atom_b": 57, "pair_type": 1}, {"atom_a": 53, "atom_b": 55, "pair_type": 1}, {"atom_a": 54, "atom_b": 56, "pair_type": 1}, {"atom_a": 58, "atom_b": 62, "pair_type": 1}, {"atom_a": 59, "atom_b": 64, "pair_type": 1}, {"atom_a": 60, "atom_b": 62, "pair_type": 1}, {"atom_a": 61, "atom_b": 63, "pair_type": 1}, {"atom_a": 65, "atom_b": 69, "pair_type": 1}, {"atom_a": 66, "atom_b": 71, "pair_type": 1}, {"atom_a": 67, "atom_b": 69, "pair_type": 1}, {"atom_a": 68, "atom_b": 70, "pair_type": 1}, {"atom_a": 72, "atom_b": 76, "pair_type": 1}, {"atom_a": 73, "atom_b": 78, "pair_type": 1}, {"atom_a": 74, "atom_b": 76, "pair_type": 1}, {"atom_a": 75, "atom_b": 77, "pair_type": 1}, {"atom_a": 79, "atom_b": 83, "pair_type": 1}, {"atom_a": 80, "atom_b": 85, "pair_type": 1}, {"atom_a": 81, "atom_b": 83, "pair_type": 1}, {"atom_a": 82, "atom_b": 84, "pair_type": 1}, {"atom_a": 86, "atom_b": 90, "pair_type": 1}, {"atom_a": 87, "atom_b": 92, "pair_type": 1}, {"atom_a": 88, "atom_b": 90, "pair_type": 1}, {"atom_a": 89, "atom_b": 91, "pair_type": 1}, {"atom_a": 93, "atom_b": 97, "pair_type": 1}, {"atom_a": 94, "atom_b": 99, "pair_type": 1}, {"atom_a": 95, "atom_b": 97, "pair_type": 1}, {"atom_a": 96, "atom_b": 98, "pair_type": 1}, {"atom_a": 100, "atom_b": 104, "pair_type": 1}, {"atom_a": 101, "atom_b": 106, "pair_type": 1}, {"atom_a": 102, "atom_b": 104, "pair_type": 1}, {"atom_a": 103, "atom_b": 105, "pair_type": 1}, {"atom_a": 107, "atom_b": 111, "pair_type": 1}, {"atom_a": 108, "atom_b": 113, "pair_type": 1}, {"atom_a": 109, "atom_b": 111, "pair_type": 1}, {"atom_a": 110, "atom_b": 112, "pair_type": 1}, {"atom_a": 114, "atom_b": 118, "pair_type": 1}, {"atom_a": 115, "atom_b": 120, "pair_type": 1}, {"atom_a": 116, "atom_b": 118, "pair_type": 1}, {"atom_a": 117, "atom_b": 119, "pair_type": 1}, {"atom_a": 121, "atom_b": 125, "pair_type": 1}, {"atom_a": 122, "atom_b": 127, "pair_type": 1}, {"atom_a": 123, "atom_b": 125, "pair_type": 1}, {"atom_a": 124, "atom_b": 126, "pair_type": 1}, {"atom_a": 128, "atom_b": 132, "pair_type": 1}, {"atom_a": 129, "atom_b": 133, "pair_type": 1}, {"atom_a": 130, "atom_b": 132, "pair_type": 1}, {"atom_a": 131, "atom_b": 134, "pair_type": 1}, {"atom_a": 137, "atom_b": 141, "pair_type": 1}, {"atom_a": 138, "atom_b": 142, "pair_type": 1}, {"atom_a": 139, "atom_b": 141, "pair_type": 1}, {"atom_a": 140, "atom_b": 144, "pair_type": 1}, {"atom_a": 140, "atom_b": 143, "pair_type": 1}], "exclusions": [], "preamble": [";----------------------------TITLE -----------------------------------------------------------------------------------------", "; None", ";", "; This file was generated at 14:05 on 2024-12-13 by", ";", "; Automatic Topology Builder", ";", "; REVISION 2024-11-20 12:06:25", ";---------------------------------------------------------------------------------------------------------------------------", "; Authors : Martin Stroet, Bertrand Caron, Alpeshkumar K. Malde, Thomas Lee, Alan E. Mark", ";", "; Institute : Molecular Dynamics group,", "; School of Chemistry and Molecular Biosciences (SCMB),", "; The University of Queensland, QLD 4072, Australia", "; URL : https://atb.uq.edu.au", "; Citations : 1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, Nair PC, Oostenbrink C, Mark AE.", "; An Automated force field Topology Builder (ATB) and repository: version 1.0.", "; Journal of Chemical Theory and Computation, 2011, 7, 4026-4037.", "; 2. Stroet M, Caron B, Visscher K, Geerke D, Malde AK, Mark AE.", "; Automated Topology Builder version 3.0: Prediction of solvation free enthalpies in water and hexane.", "; DOI:10.1021/acs.jctc.8b00768", ";", "; Disclaimer :", "; While every effort has been made to ensure the accuracy and validity of parameters provided below", "; the assignment of parameters is being based on an automated procedure combining data provided by a", "; given user as well as calculations performed using third party software. They are provided as a guide.", "; The authors of the ATB cannot guarantee that the parameters are complete or that the parameters provided", "; are appropriate for use in any specific application. Users are advised to treat these parameters with discretion", "; and to perform additional validation tests for their specific application if required. Neither the authors", "; of the ATB or The University of Queensland except any responsibly for how the parameters may be used.", ";", "; Release notes and warnings:", "; (1) The topology is based on a set of atomic coordinates and other data provided by the user after", "; after quantum mechanical optimization of the structure using different levels of theory depending on", "; the nature of the molecule.", "; (2) In some cases the automatic bond, bond angle and dihedral type assignment is ambiguous.", "; In these cases alternative type codes are provided at the end of the line.", "; (3) While bonded parameters are taken where possible from the nominated force field non-standard bond, angle and dihedral", "; type code may be incorporated in cases where an exact match could not be found. These are marked as \"non-standard\"", "; or \"uncertain\" in comments.", "; (4) In some cases it is not possible to assign an appropriate parameter automatically. \"%%\" is used as a place holder", "; for those fields that could not be determined automatically. The parameters in these fields must be assigned manually", "; before the file can be used.", ";---------------------------------------------------------------------------------------------------------------------------", "; Input Structure : LHCU", "; Output : UNITED ATOM topology", ";\tUse in conjunction with the corresponding united atom PDB file.", ";---------------------------------------------------------------------------------------------------------------------------", "; Citing this topology file", "; ATB molid: 1707355", "; ATB Topology Hash: f968d", ";---------------------------------------------------------------------------------------------------------------------------", "; Final Topology Generation was performed using:", "; A B3LYP/6-31G* optimized geometry.", "; Bonded and van der Waals parameters were taken from the GROMOS 54A7 parameter set.", "; Initial charges were estimated using the ESP method of Merz-Kollman.", "; Final charges and charge groups were generated by method described in the ATB paper.", "; If required, additional bonded parameters were generated from a Hessian matrix calculated at the B3LYP/6-31G* level of theory.", ";---------------------------------------------------------------------------------------------------------------------------", ";", ";"], "moleculetype": {"name": "LHCU", "nrexcl": 3}}, "junctions": [{"name": "to", "monomer_atom": "C51", "residue_atom": "C62"}, {"name": "from", "monomer_atom": "N7", "residue_atom": "C6"}]} \ No newline at end of file diff --git a/data_paper_examples/polyester.itp b/data_paper_examples/polyester.itp index 3f2bdcb..288c74d 100644 --- a/data_paper_examples/polyester.itp +++ b/data_paper_examples/polyester.itp @@ -190,94 +190,94 @@ E6SD 3 [ bonds ] 1 2 2 0.0972 1.9581e+07 2 3 2 0.1430 8.1800e+06 - 3 6 2 0.1520 5.4300e+06 3 4 2 0.1090 1.2300e+07 + 3 6 2 0.1520 5.4300e+06 3 5 2 0.1090 1.2300e+07 6 9 2 0.1430 8.1800e+06 - 6 8 2 0.1090 1.2300e+07 6 7 2 0.1090 1.2300e+07 + 6 8 2 0.1090 1.2300e+07 9 10 2 0.1161 1.9581e+07 10 11 2 0.1220 2.2843e+07 10 12 2 0.1500 8.3700e+06 - 12 20 2 0.1400 8.5400e+06 12 13 2 0.1400 8.5400e+06 - 13 14 2 0.1090 1.2300e+07 + 12 20 2 0.1400 8.5400e+06 13 15 2 0.1390 8.6600e+06 - 15 16 2 0.1090 1.2300e+07 + 13 14 2 0.1090 1.2300e+07 15 17 2 0.1400 8.5400e+06 - 17 22 2 0.1500 8.3700e+06 + 15 16 2 0.1090 1.2300e+07 17 18 2 0.1400 8.5400e+06 - 18 19 2 0.1090 1.2300e+07 + 17 22 2 0.1500 8.3700e+06 18 20 2 0.1390 8.6600e+06 + 18 19 2 0.1090 1.2300e+07 20 21 2 0.1090 1.2300e+07 22 23 2 0.1220 2.2843e+07 - 22 24 2 0.1161 1.9581e+07 + 22 24 2 0.1161 1.0300e+07 24 25 2 0.1430 8.1800e+06 - 25 27 2 0.1090 1.2300e+07 25 28 2 0.1520 5.4300e+06 + 25 27 2 0.1090 1.2300e+07 25 26 2 0.1090 1.2300e+07 28 30 2 0.1090 1.2300e+07 - 28 29 2 0.1090 1.2300e+07 28 31 2 0.1430 8.1800e+06 - 31 32 2 0.1161 1.0300e+07 + 28 29 2 0.1090 1.2300e+07 + 31 32 2 0.1161 1.9581e+07 32 34 2 0.1500 8.3700e+06 32 33 2 0.1220 2.2843e+07 - 34 35 2 0.1400 8.5400e+06 34 42 2 0.1400 8.5400e+06 - 35 36 2 0.1090 1.2300e+07 + 34 35 2 0.1400 8.5400e+06 35 37 2 0.1390 8.6600e+06 + 35 36 2 0.1090 1.2300e+07 37 39 2 0.1400 8.5400e+06 37 38 2 0.1090 1.2300e+07 - 39 44 2 0.1500 8.3700e+06 39 40 2 0.1400 8.5400e+06 + 39 44 2 0.1500 8.3700e+06 40 41 2 0.1090 1.2300e+07 40 42 2 0.1390 8.6600e+06 42 43 2 0.1090 1.2300e+07 - 44 46 2 0.1161 1.0300e+07 44 45 2 0.1220 2.2843e+07 + 44 46 2 0.1161 1.0300e+07 46 47 2 0.1430 8.1800e+06 - 47 48 2 0.1090 1.2300e+07 - 47 49 2 0.1090 1.2300e+07 47 50 2 0.1520 5.4300e+06 - 50 51 2 0.1090 1.2300e+07 + 47 49 2 0.1090 1.2300e+07 + 47 48 2 0.1090 1.2300e+07 50 53 2 0.1430 8.1800e+06 50 52 2 0.1090 1.2300e+07 - 53 54 2 0.1161 1.0300e+07 + 50 51 2 0.1090 1.2300e+07 + 53 54 2 0.1161 1.9581e+07 54 55 2 0.1220 2.2843e+07 54 56 2 0.1500 8.3700e+06 56 57 2 0.1400 8.5400e+06 56 64 2 0.1400 8.5400e+06 - 57 59 2 0.1390 8.6600e+06 57 58 2 0.1090 1.2300e+07 - 59 61 2 0.1400 8.5400e+06 + 57 59 2 0.1390 8.6600e+06 59 60 2 0.1090 1.2300e+07 + 59 61 2 0.1400 8.5400e+06 61 66 2 0.1500 8.3700e+06 61 62 2 0.1400 8.5400e+06 - 62 63 2 0.1090 1.2300e+07 62 64 2 0.1390 8.6600e+06 + 62 63 2 0.1090 1.2300e+07 64 65 2 0.1090 1.2300e+07 66 67 2 0.1220 2.2843e+07 - 66 68 2 0.1161 1.9581e+07 + 66 68 2 0.1161 1.0300e+07 68 69 2 0.1430 8.1800e+06 69 70 2 0.1090 1.2300e+07 69 71 2 0.1090 1.2300e+07 69 72 2 0.1520 5.4300e+06 - 72 73 2 0.1090 1.2300e+07 72 75 2 0.1430 8.1800e+06 72 74 2 0.1090 1.2300e+07 - 75 76 2 0.1161 1.0300e+07 - 76 77 2 0.1220 2.2843e+07 + 72 73 2 0.1090 1.2300e+07 + 75 76 2 0.1161 1.9581e+07 76 78 2 0.1500 8.3700e+06 - 78 86 2 0.1400 8.5400e+06 + 76 77 2 0.1220 2.2843e+07 78 79 2 0.1400 8.5400e+06 - 79 80 2 0.1090 1.2300e+07 + 78 86 2 0.1400 8.5400e+06 79 81 2 0.1390 8.6600e+06 + 79 80 2 0.1090 1.2300e+07 81 82 2 0.1090 1.2300e+07 81 83 2 0.1400 8.5400e+06 - 83 88 2 0.1500 8.3700e+06 83 84 2 0.1400 8.5400e+06 - 84 86 2 0.1390 8.6600e+06 + 83 88 2 0.1500 8.3700e+06 84 85 2 0.1090 1.2300e+07 + 84 86 2 0.1390 8.6600e+06 86 87 2 0.1090 1.2300e+07 88 90 2 0.1161 1.0300e+07 88 89 2 0.1220 2.2843e+07 @@ -288,11 +288,11 @@ E6SD 3 94 95 2 0.1090 1.2300e+07 94 96 2 0.1090 1.2300e+07 94 97 2 0.1430 8.1800e+06 - 97 98 2 0.1161 1.0300e+07 + 97 98 2 0.1161 1.9581e+07 98 100 2 0.1500 8.3700e+06 98 99 2 0.1220 2.2843e+07 - 100 108 2 0.1400 8.5400e+06 100 101 2 0.1400 8.5400e+06 + 100 108 2 0.1400 8.5400e+06 101 102 2 0.1090 1.2300e+07 101 103 2 0.1390 8.6600e+06 103 105 2 0.1400 8.5400e+06 @@ -302,74 +302,74 @@ E6SD 3 106 107 2 0.1090 1.2300e+07 106 108 2 0.1390 8.6600e+06 108 109 2 0.1090 1.2300e+07 - 110 112 2 0.1161 1.9581e+07 + 110 112 2 0.1161 1.0300e+07 110 111 2 0.1220 2.2843e+07 112 113 2 0.1430 8.1800e+06 113 116 2 0.1520 5.4300e+06 113 114 2 0.1090 1.2300e+07 113 115 2 0.1090 1.2300e+07 + 116 118 2 0.1090 1.2300e+07 116 119 2 0.1430 8.1800e+06 116 117 2 0.1090 1.2300e+07 - 116 118 2 0.1090 1.2300e+07 119 120 2 0.0972 1.9581e+07 [ pairs ] 1 5 1 - 1 4 1 1 6 1 + 1 4 1 + 2 8 1 2 7 1 2 9 1 - 2 8 1 4 9 1 4 7 1 4 8 1 - 5 9 1 5 7 1 + 5 9 1 5 8 1 - 10 15 1 - 10 18 1 10 21 1 + 10 15 1 10 14 1 + 10 18 1 11 13 1 11 20 1 - 12 16 1 12 19 1 + 12 16 1 13 22 1 13 21 1 - 14 17 1 - 14 16 1 14 20 1 + 14 16 1 + 14 17 1 15 23 1 15 19 1 - 16 22 1 16 18 1 + 16 22 1 17 21 1 18 23 1 19 22 1 19 21 1 20 22 1 - 24 30 1 24 31 1 + 24 30 1 24 29 1 - 26 30 1 26 29 1 26 31 1 - 27 30 1 - 27 29 1 + 26 30 1 27 31 1 + 27 29 1 + 27 30 1 + 32 43 1 32 40 1 32 36 1 - 32 43 1 32 37 1 33 35 1 33 42 1 - 34 41 1 34 38 1 - 35 44 1 + 34 41 1 35 43 1 - 36 39 1 - 36 38 1 + 35 44 1 36 42 1 + 36 38 1 + 36 39 1 37 45 1 37 41 1 38 44 1 @@ -383,45 +383,45 @@ E6SD 3 46 51 1 46 53 1 48 52 1 - 48 51 1 48 53 1 - 49 53 1 + 48 51 1 49 52 1 + 49 53 1 49 51 1 - 54 59 1 54 62 1 54 58 1 54 65 1 - 55 64 1 + 54 59 1 55 57 1 + 55 64 1 56 60 1 56 63 1 - 57 65 1 57 66 1 + 57 65 1 58 64 1 - 58 60 1 58 61 1 + 58 60 1 59 63 1 59 67 1 60 66 1 60 62 1 61 65 1 62 67 1 - 63 66 1 63 65 1 + 63 66 1 64 66 1 68 74 1 68 73 1 68 75 1 70 75 1 - 70 73 1 70 74 1 - 71 74 1 + 70 73 1 71 75 1 71 73 1 - 76 81 1 - 76 87 1 + 71 74 1 76 80 1 + 76 87 1 + 76 81 1 76 84 1 77 79 1 77 86 1 @@ -429,224 +429,224 @@ E6SD 3 78 85 1 79 87 1 79 88 1 - 80 86 1 80 83 1 + 80 86 1 80 82 1 81 85 1 81 89 1 - 82 88 1 82 84 1 + 82 88 1 83 87 1 84 89 1 - 85 87 1 85 88 1 + 85 87 1 86 88 1 - 90 95 1 90 97 1 90 96 1 - 92 97 1 - 92 95 1 + 90 95 1 92 96 1 + 92 95 1 + 92 97 1 93 96 1 93 95 1 93 97 1 - 98 109 1 98 106 1 - 98 102 1 98 103 1 + 98 102 1 + 98 109 1 99 108 1 99 101 1 100 104 1 100 107 1 - 101 110 1 101 109 1 + 101 110 1 + 102 104 1 102 108 1 102 105 1 - 102 104 1 - 103 111 1 103 107 1 - 104 110 1 + 103 111 1 104 106 1 + 104 110 1 105 109 1 106 111 1 - 107 110 1 107 109 1 + 107 110 1 108 110 1 + 112 119 1 112 117 1 112 118 1 - 112 119 1 113 120 1 114 119 1 114 118 1 114 117 1 115 119 1 - 115 117 1 115 118 1 + 115 117 1 117 120 1 118 120 1 [ angles ] 1 2 3 2 109.5000 4.5000e+02 - 2 3 4 2 107.5700 4.8400e+02 - 2 3 6 2 109.5000 5.2000e+02 2 3 5 2 107.5700 4.8400e+02 - 5 3 6 2 109.6000 4.5000e+02 + 2 3 6 2 109.5000 5.2000e+02 + 2 3 4 2 107.5700 4.8400e+02 4 3 6 2 109.6000 4.5000e+02 + 4 3 5 2 108.5300 4.4300e+02 3 6 9 2 109.5000 5.2000e+02 - 3 6 8 2 109.6000 4.5000e+02 3 6 7 2 109.6000 4.5000e+02 - 4 3 5 2 108.5300 4.4300e+02 - 6 9 10 2 109.5000 4.5000e+02 + 3 6 8 2 109.6000 4.5000e+02 + 5 3 6 2 109.6000 4.5000e+02 8 6 9 2 107.5700 4.8400e+02 + 6 9 10 2 109.5000 4.5000e+02 7 6 9 2 107.5700 4.8400e+02 7 6 8 2 108.5300 4.4300e+02 9 10 11 2 124.0000 7.3000e+02 9 10 12 2 115.0000 6.1000e+02 11 10 12 2 121.0000 6.8500e+02 - 10 12 20 2 120.0000 5.6000e+02 10 12 13 2 120.0000 5.6000e+02 + 10 12 20 2 120.0000 5.6000e+02 13 12 20 2 120.0000 5.6000e+02 - 12 20 18 2 120.0000 5.6000e+02 - 12 20 21 2 120.0000 5.0500e+02 12 13 14 2 120.0000 5.0500e+02 12 13 15 2 120.0000 5.6000e+02 + 12 20 21 2 120.0000 5.0500e+02 + 12 20 18 2 120.0000 5.6000e+02 + 13 15 16 2 120.0000 5.0500e+02 14 13 15 2 120.0000 5.0500e+02 13 15 17 2 120.0000 5.6000e+02 - 13 15 16 2 120.0000 5.0500e+02 - 16 15 17 2 120.0000 5.0500e+02 15 17 18 2 120.0000 5.6000e+02 15 17 22 2 120.0000 5.6000e+02 - 17 22 23 2 121.0000 6.8500e+02 + 16 15 17 2 120.0000 5.0500e+02 18 17 22 2 120.0000 5.6000e+02 - 17 22 24 2 115.0000 6.1000e+02 17 18 20 2 120.0000 5.6000e+02 17 18 19 2 120.0000 5.0500e+02 - 19 18 20 2 120.0000 5.0500e+02 + 17 22 24 2 115.0000 6.1000e+02 + 17 22 23 2 121.0000 6.8500e+02 18 20 21 2 120.0000 5.0500e+02 + 19 18 20 2 120.0000 5.0500e+02 23 22 24 2 124.0000 7.3000e+02 22 24 25 2 109.5000 4.5000e+02 24 25 27 2 107.5700 4.8400e+02 - 24 25 28 2 109.5000 5.2000e+02 24 25 26 2 107.5700 4.8400e+02 + 24 25 28 2 109.5000 5.2000e+02 27 25 28 2 109.6000 4.5000e+02 - 26 25 27 2 108.5300 4.4300e+02 - 26 25 28 2 109.6000 4.5000e+02 - 25 28 31 2 109.5000 5.2000e+02 25 28 29 2 109.6000 4.5000e+02 25 28 30 2 109.6000 4.5000e+02 + 26 25 28 2 109.6000 4.5000e+02 + 25 28 31 2 109.5000 5.2000e+02 + 26 25 27 2 108.5300 4.4300e+02 30 28 31 2 107.5700 4.8400e+02 29 28 30 2 108.5300 4.4300e+02 29 28 31 2 107.5700 4.8400e+02 28 31 32 2 109.5000 4.5000e+02 - 31 32 33 2 124.0000 7.3000e+02 31 32 34 2 115.0000 6.1000e+02 - 33 32 34 2 121.0000 6.8500e+02 + 31 32 33 2 124.0000 7.3000e+02 32 34 42 2 120.0000 5.6000e+02 32 34 35 2 120.0000 5.6000e+02 - 34 35 37 2 120.0000 5.6000e+02 - 35 34 42 2 120.0000 5.6000e+02 - 34 35 36 2 120.0000 5.0500e+02 + 33 32 34 2 121.0000 6.8500e+02 34 42 43 2 120.0000 5.0500e+02 + 35 34 42 2 120.0000 5.6000e+02 34 42 40 2 120.0000 5.6000e+02 - 36 35 37 2 120.0000 5.0500e+02 - 35 37 39 2 120.0000 5.6000e+02 + 34 35 36 2 120.0000 5.0500e+02 + 34 35 37 2 120.0000 5.6000e+02 35 37 38 2 120.0000 5.0500e+02 - 37 39 40 2 120.0000 5.6000e+02 + 35 37 39 2 120.0000 5.6000e+02 + 36 35 37 2 120.0000 5.0500e+02 37 39 44 2 120.0000 5.6000e+02 38 37 39 2 120.0000 5.0500e+02 - 39 44 46 2 115.0000 6.1000e+02 + 37 39 40 2 120.0000 5.6000e+02 40 39 44 2 120.0000 5.6000e+02 - 39 44 45 2 121.0000 6.8500e+02 - 39 40 41 2 120.0000 5.0500e+02 39 40 42 2 120.0000 5.6000e+02 + 39 40 41 2 120.0000 5.0500e+02 + 39 44 45 2 121.0000 6.8500e+02 + 39 44 46 2 115.0000 6.1000e+02 41 40 42 2 120.0000 5.0500e+02 40 42 43 2 120.0000 5.0500e+02 45 44 46 2 124.0000 7.3000e+02 44 46 47 2 109.5000 4.5000e+02 - 46 47 49 2 107.5700 4.8400e+02 - 46 47 48 2 107.5700 4.8400e+02 46 47 50 2 109.5000 5.2000e+02 + 46 47 48 2 107.5700 4.8400e+02 + 46 47 49 2 107.5700 4.8400e+02 + 47 50 53 2 109.5000 5.2000e+02 48 47 50 2 109.6000 4.5000e+02 - 48 47 49 2 108.5300 4.4300e+02 - 49 47 50 2 109.6000 4.5000e+02 47 50 52 2 109.6000 4.5000e+02 - 47 50 53 2 109.5000 5.2000e+02 47 50 51 2 109.6000 4.5000e+02 + 49 47 50 2 109.6000 4.5000e+02 + 48 47 49 2 108.5300 4.4300e+02 51 50 53 2 107.5700 4.8400e+02 - 51 50 52 2 108.5300 4.4300e+02 - 50 53 54 2 109.5000 4.5000e+02 52 50 53 2 107.5700 4.8400e+02 - 53 54 55 2 124.0000 7.3000e+02 + 50 53 54 2 109.5000 4.5000e+02 + 51 50 52 2 108.5300 4.4300e+02 53 54 56 2 115.0000 6.1000e+02 + 53 54 55 2 124.0000 7.3000e+02 55 54 56 2 121.0000 6.8500e+02 54 56 64 2 120.0000 5.6000e+02 54 56 57 2 120.0000 5.6000e+02 57 56 64 2 120.0000 5.6000e+02 56 57 58 2 120.0000 5.0500e+02 56 57 59 2 120.0000 5.6000e+02 - 56 64 62 2 120.0000 5.6000e+02 56 64 65 2 120.0000 5.0500e+02 + 56 64 62 2 120.0000 5.6000e+02 58 57 59 2 120.0000 5.0500e+02 - 57 59 61 2 120.0000 5.6000e+02 57 59 60 2 120.0000 5.0500e+02 - 59 61 62 2 120.0000 5.6000e+02 + 57 59 61 2 120.0000 5.6000e+02 60 59 61 2 120.0000 5.0500e+02 + 59 61 62 2 120.0000 5.6000e+02 59 61 66 2 120.0000 5.6000e+02 - 62 61 66 2 120.0000 5.6000e+02 - 61 66 68 2 115.0000 6.1000e+02 61 66 67 2 121.0000 6.8500e+02 - 61 62 64 2 120.0000 5.6000e+02 + 61 66 68 2 115.0000 6.1000e+02 + 62 61 66 2 120.0000 5.6000e+02 61 62 63 2 120.0000 5.0500e+02 - 63 62 64 2 120.0000 5.0500e+02 + 61 62 64 2 120.0000 5.6000e+02 62 64 65 2 120.0000 5.0500e+02 + 63 62 64 2 120.0000 5.0500e+02 67 66 68 2 124.0000 7.3000e+02 66 68 69 2 109.5000 4.5000e+02 - 68 69 70 2 107.5700 4.8400e+02 - 68 69 71 2 107.5700 4.8400e+02 68 69 72 2 109.5000 5.2000e+02 + 68 69 71 2 107.5700 4.8400e+02 + 68 69 70 2 107.5700 4.8400e+02 70 69 72 2 109.6000 4.5000e+02 70 69 71 2 108.5300 4.4300e+02 71 69 72 2 109.6000 4.5000e+02 69 72 73 2 109.6000 4.5000e+02 - 69 72 75 2 109.5000 5.2000e+02 69 72 74 2 109.6000 4.5000e+02 - 73 72 74 2 108.5300 4.4300e+02 + 69 72 75 2 109.5000 5.2000e+02 73 72 75 2 107.5700 4.8400e+02 - 72 75 76 2 109.5000 4.5000e+02 74 72 75 2 107.5700 4.8400e+02 + 72 75 76 2 109.5000 4.5000e+02 + 73 72 74 2 108.5300 4.4300e+02 75 76 77 2 124.0000 7.3000e+02 75 76 78 2 115.0000 6.1000e+02 77 76 78 2 121.0000 6.8500e+02 - 76 78 79 2 120.0000 5.6000e+02 76 78 86 2 120.0000 5.6000e+02 - 78 86 84 2 120.0000 5.6000e+02 - 78 86 87 2 120.0000 5.0500e+02 - 79 78 86 2 120.0000 5.6000e+02 + 76 78 79 2 120.0000 5.6000e+02 78 79 81 2 120.0000 5.6000e+02 78 79 80 2 120.0000 5.0500e+02 - 80 79 81 2 120.0000 5.0500e+02 + 79 78 86 2 120.0000 5.6000e+02 + 78 86 84 2 120.0000 5.6000e+02 + 78 86 87 2 120.0000 5.0500e+02 79 81 82 2 120.0000 5.0500e+02 + 80 79 81 2 120.0000 5.0500e+02 79 81 83 2 120.0000 5.6000e+02 82 81 83 2 120.0000 5.0500e+02 81 83 84 2 120.0000 5.6000e+02 81 83 88 2 120.0000 5.6000e+02 - 83 88 90 2 115.0000 6.1000e+02 - 83 88 89 2 121.0000 6.8500e+02 84 83 88 2 120.0000 5.6000e+02 83 84 86 2 120.0000 5.6000e+02 83 84 85 2 120.0000 5.0500e+02 + 83 88 90 2 115.0000 6.1000e+02 + 83 88 89 2 121.0000 6.8500e+02 85 84 86 2 120.0000 5.0500e+02 84 86 87 2 120.0000 5.0500e+02 88 90 91 2 109.5000 4.5000e+02 89 88 90 2 124.0000 7.3000e+02 90 91 92 2 107.5700 4.8400e+02 - 90 91 93 2 107.5700 4.8400e+02 90 91 94 2 109.5000 5.2000e+02 - 91 94 97 2 109.5000 5.2000e+02 + 90 91 93 2 107.5700 4.8400e+02 + 92 91 94 2 109.6000 4.5000e+02 93 91 94 2 109.6000 4.5000e+02 91 94 96 2 109.6000 4.5000e+02 91 94 95 2 109.6000 4.5000e+02 - 92 91 94 2 109.6000 4.5000e+02 + 91 94 97 2 109.5000 5.2000e+02 92 91 93 2 108.5300 4.4300e+02 95 94 96 2 108.5300 4.4300e+02 95 94 97 2 107.5700 4.8400e+02 @@ -654,14 +654,14 @@ E6SD 3 94 97 98 2 109.5000 4.5000e+02 97 98 99 2 124.0000 7.3000e+02 97 98 100 2 115.0000 6.1000e+02 + 98 100 108 2 120.0000 5.6000e+02 99 98 100 2 121.0000 6.8500e+02 98 100 101 2 120.0000 5.6000e+02 - 98 100 108 2 120.0000 5.6000e+02 - 100 108 106 2 120.0000 5.6000e+02 - 100 108 109 2 120.0000 5.0500e+02 101 100 108 2 120.0000 5.6000e+02 - 100 101 103 2 120.0000 5.6000e+02 100 101 102 2 120.0000 5.0500e+02 + 100 101 103 2 120.0000 5.6000e+02 + 100 108 106 2 120.0000 5.6000e+02 + 100 108 109 2 120.0000 5.0500e+02 102 101 103 2 120.0000 5.0500e+02 101 103 105 2 120.0000 5.6000e+02 101 103 104 2 120.0000 5.0500e+02 @@ -669,48 +669,48 @@ E6SD 3 103 105 106 2 120.0000 5.6000e+02 104 103 105 2 120.0000 5.0500e+02 105 106 107 2 120.0000 5.0500e+02 - 106 105 110 2 120.0000 5.6000e+02 105 106 108 2 120.0000 5.6000e+02 + 106 105 110 2 120.0000 5.6000e+02 105 110 112 2 115.0000 6.1000e+02 105 110 111 2 121.0000 6.8500e+02 107 106 108 2 120.0000 5.0500e+02 106 108 109 2 120.0000 5.0500e+02 - 110 112 113 2 109.5000 4.5000e+02 111 110 112 2 124.0000 7.3000e+02 - 112 113 116 2 109.5000 5.2000e+02 + 110 112 113 2 109.5000 4.5000e+02 112 113 115 2 107.5700 4.8400e+02 + 112 113 116 2 109.5000 5.2000e+02 112 113 114 2 107.5700 4.8400e+02 + 114 113 116 2 109.6000 4.5000e+02 113 116 118 2 109.6000 4.5000e+02 + 113 116 117 2 109.6000 4.5000e+02 113 116 119 2 109.5000 5.2000e+02 115 113 116 2 109.6000 4.5000e+02 - 113 116 117 2 109.6000 4.5000e+02 - 114 113 116 2 109.6000 4.5000e+02 114 113 115 2 108.5300 4.4300e+02 - 116 119 120 2 109.5000 4.5000e+02 + 117 116 118 2 108.5300 4.4300e+02 118 116 119 2 107.5700 4.8400e+02 117 116 119 2 107.5700 4.8400e+02 - 117 116 118 2 108.5300 4.4300e+02 + 116 119 120 2 109.5000 4.5000e+02 [ dihedrals ] -; GROMOS improper dihedrals +; improper dihedrals 10 9 11 12 2 0.0000 1.6736e+02 10 9 11 12 2 0.0000 1.6736e+02 12 10 13 20 2 0.0000 1.6736e+02 - 20 12 18 21 2 0.0000 1.6736e+02 13 12 14 15 2 0.0000 1.6736e+02 + 20 12 18 21 2 0.0000 1.6736e+02 15 13 16 17 2 0.0000 1.6736e+02 17 15 18 22 2 0.0000 1.6736e+02 - 22 17 23 24 2 0.0000 1.6736e+02 18 17 19 20 2 0.0000 1.6736e+02 + 22 17 23 24 2 0.0000 1.6736e+02 32 31 33 34 2 0.0000 1.6736e+02 32 31 33 34 2 0.0000 1.6736e+02 34 32 35 42 2 0.0000 1.6736e+02 - 35 34 36 37 2 0.0000 1.6736e+02 42 34 40 43 2 0.0000 1.6736e+02 + 35 34 36 37 2 0.0000 1.6736e+02 37 35 38 39 2 0.0000 1.6736e+02 39 37 40 44 2 0.0000 1.6736e+02 - 44 39 45 46 2 0.0000 1.6736e+02 40 39 41 42 2 0.0000 1.6736e+02 + 44 39 45 46 2 0.0000 1.6736e+02 54 53 55 56 2 0.0000 1.6736e+02 54 53 55 56 2 0.0000 1.6736e+02 56 54 57 64 2 0.0000 1.6736e+02 @@ -723,17 +723,17 @@ E6SD 3 76 75 77 78 2 0.0000 1.6736e+02 76 75 77 78 2 0.0000 1.6736e+02 78 76 79 86 2 0.0000 1.6736e+02 - 86 78 84 87 2 0.0000 1.6736e+02 79 78 80 81 2 0.0000 1.6736e+02 + 86 78 84 87 2 0.0000 1.6736e+02 81 79 82 83 2 0.0000 1.6736e+02 83 81 84 88 2 0.0000 1.6736e+02 - 88 83 89 90 2 0.0000 1.6736e+02 84 83 85 86 2 0.0000 1.6736e+02 + 88 83 89 90 2 0.0000 1.6736e+02 98 97 99 100 2 0.0000 1.6736e+02 98 97 99 100 2 0.0000 1.6736e+02 100 98 101 108 2 0.0000 1.6736e+02 - 108 100 106 109 2 0.0000 1.6736e+02 101 100 102 103 2 0.0000 1.6736e+02 + 108 100 106 109 2 0.0000 1.6736e+02 103 101 104 105 2 0.0000 1.6736e+02 105 103 106 110 2 0.0000 1.6736e+02 106 105 107 108 2 0.0000 1.6736e+02 @@ -744,10 +744,10 @@ E6SD 3 2 3 6 9 1 0.0000 5.9200e+00 3 3 6 9 10 1 0.0000 1.2600e+00 3 11 10 12 13 1 180.0000 5.8600e+00 2 - 13 12 20 18 1 180.0000 4.1800e+01 2 20 12 13 15 1 180.0000 4.1800e+01 2 - 17 18 20 12 1 180.0000 4.1800e+01 2 + 13 12 20 18 1 180.0000 4.1800e+01 2 12 13 15 17 1 180.0000 4.1800e+01 2 + 17 18 20 12 1 180.0000 4.1800e+01 2 13 15 17 18 1 180.0000 4.1800e+01 2 15 17 18 20 1 180.0000 4.1800e+01 2 15 17 22 23 1 180.0000 5.8600e+00 2 @@ -755,19 +755,19 @@ E6SD 3 24 25 28 31 1 0.0000 5.9200e+00 3 25 28 31 32 1 0.0000 1.2600e+00 3 33 32 34 35 1 180.0000 5.8600e+00 2 - 34 35 37 39 1 180.0000 4.1800e+01 2 - 42 34 35 37 1 180.0000 4.1800e+01 2 35 34 42 40 1 180.0000 4.1800e+01 2 + 42 34 35 37 1 180.0000 4.1800e+01 2 39 40 42 34 1 180.0000 4.1800e+01 2 + 34 35 37 39 1 180.0000 4.1800e+01 2 35 37 39 40 1 180.0000 4.1800e+01 2 - 37 39 40 42 1 180.0000 4.1800e+01 2 37 39 44 45 1 180.0000 5.8600e+00 2 + 37 39 40 42 1 180.0000 4.1800e+01 2 44 46 47 50 1 0.0000 1.2600e+00 3 46 47 50 53 1 0.0000 5.9200e+00 3 47 50 53 54 1 0.0000 1.2600e+00 3 55 54 56 57 1 180.0000 5.8600e+00 2 - 57 56 64 62 1 180.0000 4.1800e+01 2 64 56 57 59 1 180.0000 4.1800e+01 2 + 57 56 64 62 1 180.0000 4.1800e+01 2 56 57 59 61 1 180.0000 4.1800e+01 2 61 62 64 56 1 180.0000 4.1800e+01 2 57 59 61 62 1 180.0000 4.1800e+01 2 @@ -777,10 +777,10 @@ E6SD 3 68 69 72 75 1 0.0000 5.9200e+00 3 69 72 75 76 1 0.0000 1.2600e+00 3 77 76 78 79 1 180.0000 5.8600e+00 2 - 83 84 86 78 1 180.0000 4.1800e+01 2 - 79 78 86 84 1 180.0000 4.1800e+01 2 86 78 79 81 1 180.0000 4.1800e+01 2 78 79 81 83 1 180.0000 4.1800e+01 2 + 79 78 86 84 1 180.0000 4.1800e+01 2 + 83 84 86 78 1 180.0000 4.1800e+01 2 79 81 83 84 1 180.0000 4.1800e+01 2 81 83 84 86 1 180.0000 4.1800e+01 2 81 83 88 89 1 180.0000 5.8600e+00 2 @@ -789,9 +789,9 @@ E6SD 3 91 94 97 98 1 0.0000 1.2600e+00 3 99 98 100 101 1 180.0000 5.8600e+00 2 101 100 108 106 1 180.0000 4.1800e+01 2 - 105 106 108 100 1 180.0000 4.1800e+01 2 108 100 101 103 1 180.0000 4.1800e+01 2 100 101 103 105 1 180.0000 4.1800e+01 2 + 105 106 108 100 1 180.0000 4.1800e+01 2 101 103 105 106 1 180.0000 4.1800e+01 2 103 105 110 111 1 180.0000 5.8600e+00 2 103 105 106 108 1 180.0000 4.1800e+01 2 diff --git a/data_paper_examples/polyester.png b/data_paper_examples/polyester.png index 0bb9a0e..d1a8d29 100644 Binary files a/data_paper_examples/polyester.png and b/data_paper_examples/polyester.png differ diff --git a/data_paper_examples/six_arm_star_monomer_build.itp b/data_paper_examples/six_arm_star_monomer_build.itp index c859cf5..f5d3261 100644 --- a/data_paper_examples/six_arm_star_monomer_build.itp +++ b/data_paper_examples/six_arm_star_monomer_build.itp @@ -84,199 +84,199 @@ BWD8 3 16 HC 3 BWD8 H2 16 0.018839 1.0080 17 C 3 BWD8 C2 17 -0.237161 12.0110 18 HC 3 BWD8 H5 18 0.126839 1.0080 - 19 CPos 4 BWD8 C1 19 0.407123 12.0110 - 20 HC 4 BWD8 H2 20 0.006123 1.0080 - 21 C 4 BWD8 C2 21 -0.249877 12.0110 - 22 HC 4 BWD8 H4 22 0.114123 1.0080 - 23 HC 4 BWD8 H5 23 0.114123 1.0080 - 24 OAlc 5 BWD8 O1 24 -0.615407 15.9994 - 25 CPos 5 BWD8 C1 25 0.435593 12.0110 - 26 HC 5 BWD8 H1 26 0.034593 1.0080 - 27 HC 5 BWD8 H2 27 0.034593 1.0080 - 28 HC 5 BWD8 H4 28 0.142593 1.0080 - 29 HC 5 BWD8 H5 29 0.142593 1.0080 - 30 C 5 BWD8 C2 30 -0.221407 12.0110 - 31 OAlc 5 6ZJN OAB 31 -0.626407 15.9994 - 32 CPos 5 6ZJN CAD 32 0.303593 12.0110 - 33 HC 5 6ZJN HAF 33 0.077593 1.0080 - 34 HC 5 6ZJN HAG 34 0.077593 1.0080 - 35 C 5 6ZJN CAC 35 0.138593 12.0110 - 36 HC 5 6ZJN HAD 36 0.063593 1.0080 - 37 HC 5 6ZJN HAE 37 0.063593 1.0080 - 38 C 5 6ZJN CAA 38 -0.218407 12.0110 - 39 HC 5 6ZJN HAA 39 0.133593 1.0080 - 40 HC 5 6ZJN HAB 40 0.133593 1.0080 - 41 HC 5 6ZJN HAC 41 0.133593 1.0080 - 42 OAlc 6 BWD8 O1 42 -0.622292 15.9994 - 43 CPos 6 BWD8 C1 43 0.428708 12.0110 - 44 HC 6 BWD8 H1 44 0.027708 1.0080 - 45 HC 6 BWD8 H2 45 0.027708 1.0080 - 46 HC 6 BWD8 H4 46 0.135708 1.0080 - 47 HC 6 BWD8 H5 47 0.135708 1.0080 - 48 C 6 BWD8 C2 48 -0.228292 12.0110 - 49 OAlc 6 6ZJN OAB 49 -0.633292 15.9994 - 50 CPos 6 6ZJN CAD 50 0.296708 12.0110 - 51 HC 6 6ZJN HAF 51 0.070708 1.0080 - 52 HC 6 6ZJN HAG 52 0.070708 1.0080 - 53 C 6 6ZJN CAC 53 0.131708 12.0110 - 54 HC 6 6ZJN HAD 54 0.056708 1.0080 - 55 HC 6 6ZJN HAE 55 0.056708 1.0080 - 56 C 6 6ZJN CAA 56 -0.225292 12.0110 - 57 HC 6 6ZJN HAA 57 0.126708 1.0080 - 58 HC 6 6ZJN HAB 58 0.126708 1.0080 - 59 HC 6 6ZJN HAC 59 0.126708 1.0080 - 60 OAlc 7 BWD8 O1 60 -0.621324 15.9994 - 61 CPos 7 BWD8 C1 61 0.429676 12.0110 - 62 HC 7 BWD8 H1 62 0.028676 1.0080 - 63 HC 7 BWD8 H2 63 0.028676 1.0080 - 64 HC 7 BWD8 H4 64 0.136676 1.0080 - 65 HC 7 BWD8 H5 65 0.136676 1.0080 - 66 C 7 BWD8 C2 66 -0.227324 12.0110 - 67 OAlc 7 6ZJN OAB 67 -0.632324 15.9994 - 68 CPos 7 6ZJN CAD 68 0.297676 12.0110 - 69 HC 7 6ZJN HAF 69 0.071676 1.0080 - 70 HC 7 6ZJN HAG 70 0.071676 1.0080 - 71 C 7 6ZJN CAC 71 0.132676 12.0110 - 72 HC 7 6ZJN HAD 72 0.057676 1.0080 - 73 HC 7 6ZJN HAE 73 0.057676 1.0080 - 74 C 7 6ZJN CAA 74 -0.224324 12.0110 - 75 HC 7 6ZJN HAA 75 0.127676 1.0080 - 76 HC 7 6ZJN HAB 76 0.127676 1.0080 - 77 HC 7 6ZJN HAC 77 0.127676 1.0080 - 78 OAlc 8 BWD8 O1 78 -0.620849 15.9994 - 79 CPos 8 BWD8 C1 79 0.430151 12.0110 - 80 HC 8 BWD8 H1 80 0.029151 1.0080 - 81 HC 8 BWD8 H2 81 0.029151 1.0080 - 82 HC 8 BWD8 H4 82 0.137151 1.0080 - 83 HC 8 BWD8 H5 83 0.137151 1.0080 - 84 C 8 BWD8 C2 84 -0.226849 12.0110 - 85 OAlc 8 6ZJN OAB 85 -0.631849 15.9994 - 86 CPos 8 6ZJN CAD 86 0.298151 12.0110 - 87 HC 8 6ZJN HAF 87 0.072151 1.0080 - 88 HC 8 6ZJN HAG 88 0.072151 1.0080 - 89 C 8 6ZJN CAC 89 0.133151 12.0110 - 90 HC 8 6ZJN HAD 90 0.058151 1.0080 - 91 HC 8 6ZJN HAE 91 0.058151 1.0080 - 92 C 8 6ZJN CAA 92 -0.223849 12.0110 - 93 HC 8 6ZJN HAA 93 0.128151 1.0080 - 94 HC 8 6ZJN HAB 94 0.128151 1.0080 - 95 HC 8 6ZJN HAC 95 0.128151 1.0080 - 96 OAlc 9 BWD8 O1 96 -0.624696 15.9994 - 97 CPos 9 BWD8 C1 97 0.426304 12.0110 - 98 HC 9 BWD8 H1 98 0.025304 1.0080 - 99 HC 9 BWD8 H2 99 0.025304 1.0080 - 100 HC 9 BWD8 H4 100 0.133304 1.0080 - 101 HC 9 BWD8 H5 101 0.133304 1.0080 - 102 C 9 BWD8 C2 102 -0.230696 12.0110 - 103 OAlc 9 6ZJN OAB 103 -0.635696 15.9994 - 104 CPos 9 6ZJN CAD 104 0.294304 12.0110 - 105 HC 9 6ZJN HAF 105 0.068304 1.0080 - 106 HC 9 6ZJN HAG 106 0.068304 1.0080 - 107 C 9 6ZJN CAC 107 0.129304 12.0110 - 108 HC 9 6ZJN HAD 108 0.054304 1.0080 - 109 HC 9 6ZJN HAE 109 0.054304 1.0080 - 110 C 9 6ZJN CAA 110 -0.227696 12.0110 - 111 HC 9 6ZJN HAA 111 0.124304 1.0080 - 112 HC 9 6ZJN HAB 112 0.124304 1.0080 - 113 HC 9 6ZJN HAC 113 0.124304 1.0080 - 114 OAlc 10 BWD8 O1 114 -0.640419 15.9994 - 115 CPos 10 BWD8 C1 115 0.410581 12.0110 - 116 HC 10 BWD8 H1 116 0.009581 1.0080 - 117 HC 10 BWD8 H2 117 0.009581 1.0080 - 118 HC 10 BWD8 H4 118 0.117581 1.0080 - 119 HC 10 BWD8 H5 119 0.117581 1.0080 - 120 C 10 BWD8 C2 120 -0.246419 12.0110 - 121 OAlc 10 6ZJN OAB 121 -0.651419 15.9994 - 122 CPos 10 6ZJN CAD 122 0.278581 12.0110 - 123 HC 10 6ZJN HAF 123 0.052581 1.0080 - 124 HC 10 6ZJN HAG 124 0.052581 1.0080 - 125 C 10 6ZJN CAC 125 0.113581 12.0110 - 126 HC 10 6ZJN HAD 126 0.038581 1.0080 - 127 HC 10 6ZJN HAE 127 0.038581 1.0080 - 128 C 10 6ZJN CAA 128 -0.243419 12.0110 - 129 HC 10 6ZJN HAA 129 0.108581 1.0080 - 130 HC 10 6ZJN HAB 130 0.108581 1.0080 - 131 HC 10 6ZJN HAC 131 0.108581 1.0080 + 19 CPos 4 BWD8 C1 19 0.406948 12.0110 + 20 HC 4 BWD8 H2 20 0.005948 1.0080 + 21 C 4 BWD8 C2 21 -0.250052 12.0110 + 22 HC 4 BWD8 H4 22 0.113948 1.0080 + 23 HC 4 BWD8 H5 23 0.113948 1.0080 + 24 OAlc 5 BWD8 O1 24 -0.615466 15.9994 + 25 CPos 5 BWD8 C1 25 0.435534 12.0110 + 26 HC 5 BWD8 H1 26 0.034534 1.0080 + 27 HC 5 BWD8 H2 27 0.034534 1.0080 + 28 HC 5 BWD8 H4 28 0.142534 1.0080 + 29 HC 5 BWD8 H5 29 0.142534 1.0080 + 30 C 5 BWD8 C2 30 -0.221466 12.0110 + 31 OAlc 5 6ZJN OAB 31 -0.626466 15.9994 + 32 CPos 5 6ZJN CAD 32 0.303534 12.0110 + 33 HC 5 6ZJN HAF 33 0.077534 1.0080 + 34 HC 5 6ZJN HAG 34 0.077534 1.0080 + 35 C 5 6ZJN CAC 35 0.138534 12.0110 + 36 HC 5 6ZJN HAD 36 0.063534 1.0080 + 37 HC 5 6ZJN HAE 37 0.063534 1.0080 + 38 C 5 6ZJN CAA 38 -0.218466 12.0110 + 39 HC 5 6ZJN HAA 39 0.133534 1.0080 + 40 HC 5 6ZJN HAB 40 0.133534 1.0080 + 41 HC 5 6ZJN HAC 41 0.133534 1.0080 + 42 OAlc 6 BWD8 O1 42 -0.621700 15.9994 + 43 CPos 6 BWD8 C1 43 0.429300 12.0110 + 44 HC 6 BWD8 H1 44 0.028300 1.0080 + 45 HC 6 BWD8 H2 45 0.028300 1.0080 + 46 HC 6 BWD8 H4 46 0.136300 1.0080 + 47 HC 6 BWD8 H5 47 0.136300 1.0080 + 48 C 6 BWD8 C2 48 -0.227700 12.0110 + 49 OAlc 6 6ZJN OAB 49 -0.632700 15.9994 + 50 CPos 6 6ZJN CAD 50 0.297300 12.0110 + 51 HC 6 6ZJN HAF 51 0.071300 1.0080 + 52 HC 6 6ZJN HAG 52 0.071300 1.0080 + 53 C 6 6ZJN CAC 53 0.132300 12.0110 + 54 HC 6 6ZJN HAD 54 0.057300 1.0080 + 55 HC 6 6ZJN HAE 55 0.057300 1.0080 + 56 C 6 6ZJN CAA 56 -0.224700 12.0110 + 57 HC 6 6ZJN HAA 57 0.127300 1.0080 + 58 HC 6 6ZJN HAB 58 0.127300 1.0080 + 59 HC 6 6ZJN HAC 59 0.127300 1.0080 + 60 OAlc 7 BWD8 O1 60 -0.620849 15.9994 + 61 CPos 7 BWD8 C1 61 0.430151 12.0110 + 62 HC 7 BWD8 H1 62 0.029151 1.0080 + 63 HC 7 BWD8 H2 63 0.029151 1.0080 + 64 HC 7 BWD8 H4 64 0.137151 1.0080 + 65 HC 7 BWD8 H5 65 0.137151 1.0080 + 66 C 7 BWD8 C2 66 -0.226849 12.0110 + 67 OAlc 7 6ZJN OAB 67 -0.631849 15.9994 + 68 CPos 7 6ZJN CAD 68 0.298151 12.0110 + 69 HC 7 6ZJN HAF 69 0.072151 1.0080 + 70 HC 7 6ZJN HAG 70 0.072151 1.0080 + 71 C 7 6ZJN CAC 71 0.133151 12.0110 + 72 HC 7 6ZJN HAD 72 0.058151 1.0080 + 73 HC 7 6ZJN HAE 73 0.058151 1.0080 + 74 C 7 6ZJN CAA 74 -0.223849 12.0110 + 75 HC 7 6ZJN HAA 75 0.128151 1.0080 + 76 HC 7 6ZJN HAB 76 0.128151 1.0080 + 77 HC 7 6ZJN HAC 77 0.128151 1.0080 + 78 OAlc 8 BWD8 O1 78 -0.621324 15.9994 + 79 CPos 8 BWD8 C1 79 0.429676 12.0110 + 80 HC 8 BWD8 H1 80 0.028676 1.0080 + 81 HC 8 BWD8 H2 81 0.028676 1.0080 + 82 HC 8 BWD8 H4 82 0.136676 1.0080 + 83 HC 8 BWD8 H5 83 0.136676 1.0080 + 84 C 8 BWD8 C2 84 -0.227324 12.0110 + 85 OAlc 8 6ZJN OAB 85 -0.632324 15.9994 + 86 CPos 8 6ZJN CAD 86 0.297676 12.0110 + 87 HC 8 6ZJN HAF 87 0.071676 1.0080 + 88 HC 8 6ZJN HAG 88 0.071676 1.0080 + 89 C 8 6ZJN CAC 89 0.132676 12.0110 + 90 HC 8 6ZJN HAD 90 0.057676 1.0080 + 91 HC 8 6ZJN HAE 91 0.057676 1.0080 + 92 C 8 6ZJN CAA 92 -0.224324 12.0110 + 93 HC 8 6ZJN HAA 93 0.127676 1.0080 + 94 HC 8 6ZJN HAB 94 0.127676 1.0080 + 95 HC 8 6ZJN HAC 95 0.127676 1.0080 + 96 OAlc 9 BWD8 O1 96 -0.625175 15.9994 + 97 CPos 9 BWD8 C1 97 0.425825 12.0110 + 98 HC 9 BWD8 H1 98 0.024825 1.0080 + 99 HC 9 BWD8 H2 99 0.024825 1.0080 + 100 HC 9 BWD8 H4 100 0.132825 1.0080 + 101 HC 9 BWD8 H5 101 0.132825 1.0080 + 102 C 9 BWD8 C2 102 -0.231175 12.0110 + 103 OAlc 9 6ZJN OAB 103 -0.636175 15.9994 + 104 CPos 9 6ZJN CAD 104 0.293825 12.0110 + 105 HC 9 6ZJN HAF 105 0.067825 1.0080 + 106 HC 9 6ZJN HAG 106 0.067825 1.0080 + 107 C 9 6ZJN CAC 107 0.128825 12.0110 + 108 HC 9 6ZJN HAD 108 0.053825 1.0080 + 109 HC 9 6ZJN HAE 109 0.053825 1.0080 + 110 C 9 6ZJN CAA 110 -0.228175 12.0110 + 111 HC 9 6ZJN HAA 111 0.123825 1.0080 + 112 HC 9 6ZJN HAB 112 0.123825 1.0080 + 113 HC 9 6ZJN HAC 113 0.123825 1.0080 + 114 OAlc 10 BWD8 O1 114 -0.640424 15.9994 + 115 CPos 10 BWD8 C1 115 0.410576 12.0110 + 116 HC 10 BWD8 H1 116 0.009576 1.0080 + 117 HC 10 BWD8 H2 117 0.009576 1.0080 + 118 HC 10 BWD8 H4 118 0.117576 1.0080 + 119 HC 10 BWD8 H5 119 0.117576 1.0080 + 120 C 10 BWD8 C2 120 -0.246424 12.0110 + 121 OAlc 10 6ZJN OAB 121 -0.651424 15.9994 + 122 CPos 10 6ZJN CAD 122 0.278576 12.0110 + 123 HC 10 6ZJN HAF 123 0.052576 1.0080 + 124 HC 10 6ZJN HAG 124 0.052576 1.0080 + 125 C 10 6ZJN CAC 125 0.113576 12.0110 + 126 HC 10 6ZJN HAD 126 0.038576 1.0080 + 127 HC 10 6ZJN HAE 127 0.038576 1.0080 + 128 C 10 6ZJN CAA 128 -0.243424 12.0110 + 129 HC 10 6ZJN HAA 129 0.108576 1.0080 + 130 HC 10 6ZJN HAB 130 0.108576 1.0080 + 131 HC 10 6ZJN HAC 131 0.108576 1.0080 [ bonds ] 1 2 2 0.1430 8.1800e+06 - 1 11 2 0.1031 1.2300e+07 - 2 4 2 0.1100 1.2100e+07 - 2 5 2 0.1520 5.4300e+06 + 1 11 2 0.1031 1.9581e+07 2 3 2 0.1100 1.2100e+07 - 5 42 2 0.1031 1.2300e+07 - 5 60 2 0.1031 1.2300e+07 + 2 5 2 0.1520 5.4300e+06 + 2 4 2 0.1100 1.2100e+07 5 6 2 0.1090 1.2300e+07 + 5 96 2 0.1031 1.2300e+07 + 5 24 2 0.1031 1.2300e+07 7 8 2 0.1430 8.1800e+06 - 7 17 2 0.1031 1.2300e+07 - 8 10 2 0.1100 1.2100e+07 - 8 11 2 0.1520 5.4300e+06 + 7 17 2 0.1031 1.9581e+07 8 9 2 0.1100 1.2100e+07 + 8 11 2 0.1520 5.4300e+06 + 8 10 2 0.1100 1.2100e+07 11 78 2 0.1031 1.2300e+07 11 12 2 0.1090 1.2300e+07 - 13 19 2 0.1201 8.1800e+06 + 13 19 2 0.1201 1.9581e+07 13 14 2 0.1430 8.1800e+06 - 14 16 2 0.1100 1.2100e+07 14 17 2 0.1520 5.4300e+06 + 14 16 2 0.1100 1.2100e+07 14 15 2 0.1100 1.2100e+07 - 17 96 2 0.1031 1.2300e+07 + 17 60 2 0.1031 1.2300e+07 17 18 2 0.1090 1.2300e+07 + 19 114 2 0.1036 1.2100e+07 19 20 2 0.1100 1.2100e+07 - 19 114 2 0.1036 1.9581e+07 19 21 2 0.1520 5.4300e+06 - 21 23 2 0.1090 1.2300e+07 - 21 24 2 0.1031 1.9581e+07 + 21 42 2 0.1031 1.2300e+07 21 22 2 0.1090 1.2300e+07 + 21 23 2 0.1090 1.2300e+07 24 25 2 0.1430 8.1800e+06 - 25 27 2 0.1100 1.2100e+07 - 25 30 2 0.1520 5.4300e+06 25 26 2 0.1100 1.2100e+07 + 25 30 2 0.1520 5.4300e+06 + 25 27 2 0.1100 1.2100e+07 28 30 2 0.1090 1.2300e+07 29 30 2 0.1090 1.2300e+07 30 31 2 0.1031 1.2300e+07 31 32 2 0.1430 8.1800e+06 + 32 35 2 0.1530 7.1500e+06 32 34 2 0.1090 1.2300e+07 32 33 2 0.1090 1.2300e+07 - 32 35 2 0.1530 7.1500e+06 - 35 37 2 0.1090 1.2300e+07 - 35 36 2 0.1090 1.2300e+07 35 38 2 0.1530 7.1500e+06 - 38 39 2 0.1090 1.2300e+07 + 35 36 2 0.1090 1.2300e+07 + 35 37 2 0.1090 1.2300e+07 38 41 2 0.1090 1.2300e+07 38 40 2 0.1090 1.2300e+07 + 38 39 2 0.1090 1.2300e+07 42 43 2 0.1430 8.1800e+06 + 43 44 2 0.1100 1.2100e+07 43 45 2 0.1100 1.2100e+07 43 48 2 0.1520 5.4300e+06 - 43 44 2 0.1100 1.2100e+07 46 48 2 0.1090 1.2300e+07 47 48 2 0.1090 1.2300e+07 48 49 2 0.1031 1.2300e+07 49 50 2 0.1430 8.1800e+06 - 50 53 2 0.1530 7.1500e+06 - 50 52 2 0.1090 1.2300e+07 50 51 2 0.1090 1.2300e+07 - 53 54 2 0.1090 1.2300e+07 - 53 56 2 0.1530 7.1500e+06 + 50 52 2 0.1090 1.2300e+07 + 50 53 2 0.1530 7.1500e+06 53 55 2 0.1090 1.2300e+07 - 56 58 2 0.1090 1.2300e+07 + 53 56 2 0.1530 7.1500e+06 + 53 54 2 0.1090 1.2300e+07 56 59 2 0.1090 1.2300e+07 56 57 2 0.1090 1.2300e+07 + 56 58 2 0.1090 1.2300e+07 60 61 2 0.1430 8.1800e+06 + 61 66 2 0.1520 5.4300e+06 61 63 2 0.1100 1.2100e+07 61 62 2 0.1100 1.2100e+07 - 61 66 2 0.1520 5.4300e+06 64 66 2 0.1090 1.2300e+07 65 66 2 0.1090 1.2300e+07 66 67 2 0.1031 1.2300e+07 67 68 2 0.1430 8.1800e+06 - 68 69 2 0.1090 1.2300e+07 68 71 2 0.1530 7.1500e+06 + 68 69 2 0.1090 1.2300e+07 68 70 2 0.1090 1.2300e+07 - 71 72 2 0.1090 1.2300e+07 71 73 2 0.1090 1.2300e+07 71 74 2 0.1530 7.1500e+06 - 74 77 2 0.1090 1.2300e+07 + 71 72 2 0.1090 1.2300e+07 74 76 2 0.1090 1.2300e+07 + 74 77 2 0.1090 1.2300e+07 74 75 2 0.1090 1.2300e+07 78 79 2 0.1430 8.1800e+06 79 81 2 0.1100 1.2100e+07 @@ -286,49 +286,49 @@ BWD8 3 83 84 2 0.1090 1.2300e+07 84 85 2 0.1031 1.2300e+07 85 86 2 0.1430 8.1800e+06 - 86 89 2 0.1530 7.1500e+06 - 86 87 2 0.1090 1.2300e+07 86 88 2 0.1090 1.2300e+07 + 86 87 2 0.1090 1.2300e+07 + 86 89 2 0.1530 7.1500e+06 89 92 2 0.1530 7.1500e+06 89 90 2 0.1090 1.2300e+07 89 91 2 0.1090 1.2300e+07 - 92 94 2 0.1090 1.2300e+07 - 92 93 2 0.1090 1.2300e+07 92 95 2 0.1090 1.2300e+07 + 92 93 2 0.1090 1.2300e+07 + 92 94 2 0.1090 1.2300e+07 96 97 2 0.1430 8.1800e+06 - 97 99 2 0.1100 1.2100e+07 97 98 2 0.1100 1.2100e+07 97 102 2 0.1520 5.4300e+06 + 97 99 2 0.1100 1.2100e+07 100 102 2 0.1090 1.2300e+07 101 102 2 0.1090 1.2300e+07 102 103 2 0.1031 1.2300e+07 103 104 2 0.1430 8.1800e+06 - 104 106 2 0.1090 1.2300e+07 104 105 2 0.1090 1.2300e+07 + 104 106 2 0.1090 1.2300e+07 104 107 2 0.1530 7.1500e+06 + 107 108 2 0.1090 1.2300e+07 107 110 2 0.1530 7.1500e+06 107 109 2 0.1090 1.2300e+07 - 107 108 2 0.1090 1.2300e+07 - 110 111 2 0.1090 1.2300e+07 - 110 112 2 0.1090 1.2300e+07 110 113 2 0.1090 1.2300e+07 + 110 112 2 0.1090 1.2300e+07 + 110 111 2 0.1090 1.2300e+07 114 115 2 0.1430 8.1800e+06 115 117 2 0.1100 1.2100e+07 - 115 116 2 0.1100 1.2100e+07 115 120 2 0.1520 5.4300e+06 + 115 116 2 0.1100 1.2100e+07 118 120 2 0.1090 1.2300e+07 119 120 2 0.1090 1.2300e+07 120 121 2 0.1031 1.2300e+07 121 122 2 0.1430 8.1800e+06 - 122 123 2 0.1090 1.2300e+07 122 125 2 0.1530 7.1500e+06 122 124 2 0.1090 1.2300e+07 + 122 123 2 0.1090 1.2300e+07 125 127 2 0.1090 1.2300e+07 - 125 126 2 0.1090 1.2300e+07 125 128 2 0.1530 7.1500e+06 - 128 130 2 0.1090 1.2300e+07 + 125 126 2 0.1090 1.2300e+07 128 131 2 0.1090 1.2300e+07 128 129 2 0.1090 1.2300e+07 + 128 130 2 0.1090 1.2300e+07 [ pairs ] 1 6 1 @@ -340,53 +340,53 @@ BWD8 3 13 18 1 15 18 1 16 18 1 - 20 22 1 20 23 1 - 24 29 1 + 20 22 1 24 28 1 - 26 28 1 + 24 29 1 26 29 1 - 27 29 1 + 26 28 1 27 28 1 - 31 37 1 + 27 29 1 31 38 1 31 36 1 + 31 37 1 32 41 1 32 39 1 32 40 1 33 36 1 - 33 37 1 33 38 1 + 33 37 1 34 38 1 - 34 37 1 34 36 1 + 34 37 1 36 41 1 - 36 40 1 36 39 1 + 36 40 1 37 41 1 37 40 1 37 39 1 - 42 47 1 42 46 1 + 42 47 1 44 46 1 44 47 1 45 46 1 45 47 1 - 49 54 1 - 49 56 1 49 55 1 + 49 56 1 + 49 54 1 50 57 1 50 59 1 50 58 1 + 51 56 1 51 55 1 51 54 1 - 51 56 1 - 52 56 1 52 55 1 + 52 56 1 52 54 1 54 57 1 - 54 59 1 54 58 1 + 54 59 1 55 58 1 55 59 1 55 57 1 @@ -396,226 +396,226 @@ BWD8 3 62 65 1 63 64 1 63 65 1 - 67 73 1 67 74 1 67 72 1 - 68 77 1 - 68 75 1 + 67 73 1 68 76 1 - 69 73 1 + 68 75 1 + 68 77 1 69 72 1 69 74 1 - 70 72 1 + 69 73 1 70 74 1 + 70 72 1 70 73 1 72 77 1 - 72 76 1 72 75 1 + 72 76 1 73 76 1 73 77 1 73 75 1 - 78 82 1 78 83 1 - 80 83 1 + 78 82 1 80 82 1 + 80 83 1 81 83 1 81 82 1 85 91 1 - 85 90 1 85 92 1 - 86 94 1 - 86 93 1 + 85 90 1 86 95 1 + 86 93 1 + 86 94 1 87 91 1 87 90 1 87 92 1 88 92 1 - 88 91 1 88 90 1 - 90 95 1 + 88 91 1 90 94 1 + 90 95 1 90 93 1 - 91 93 1 91 95 1 + 91 93 1 91 94 1 96 100 1 96 101 1 98 101 1 98 100 1 - 99 100 1 99 101 1 + 99 100 1 103 108 1 - 103 110 1 103 109 1 - 104 113 1 + 103 110 1 104 112 1 + 104 113 1 104 111 1 105 109 1 - 105 110 1 105 108 1 - 106 110 1 - 106 108 1 + 105 110 1 106 109 1 - 108 112 1 + 106 108 1 + 106 110 1 108 111 1 108 113 1 + 108 112 1 109 111 1 109 112 1 109 113 1 114 119 1 114 118 1 - 116 119 1 116 118 1 - 117 118 1 + 116 119 1 117 119 1 - 121 126 1 + 117 118 1 121 128 1 + 121 126 1 121 127 1 + 122 131 1 122 129 1 122 130 1 - 122 131 1 123 127 1 123 128 1 123 126 1 - 124 127 1 124 128 1 124 126 1 + 124 127 1 126 131 1 - 126 130 1 126 129 1 + 126 130 1 127 129 1 - 127 131 1 127 130 1 + 127 131 1 [ angles ] 1 2 3 2 111.0000 5.3000e+02 - 1 2 4 2 111.0000 5.3000e+02 - 2 1 11 2 109.5000 4.5000e+02 1 2 5 2 109.5000 5.2000e+02 + 2 1 11 2 109.5000 4.5000e+02 + 1 2 4 2 111.0000 5.3000e+02 1 11 78 2 108.5300 4.4300e+02 1 11 8 2 110.3000 5.2400e+02 - 4 2 5 2 110.3000 5.2400e+02 - 3 2 4 2 107.5700 4.8400e+02 + 1 11 12 2 108.5300 4.4300e+02 3 2 5 2 110.3000 5.2400e+02 - 2 5 42 2 110.3000 5.2400e+02 - 2 5 60 2 110.3000 5.2400e+02 + 3 2 4 2 107.5700 4.8400e+02 + 2 5 24 2 110.3000 5.2400e+02 + 2 5 96 2 110.3000 5.2400e+02 2 5 6 2 110.3000 5.2400e+02 - 42 5 60 2 108.5300 4.4300e+02 - 5 42 43 2 109.5000 4.5000e+02 - 6 5 42 2 108.5300 4.4300e+02 - 6 5 60 2 108.5300 4.4300e+02 - 5 60 61 2 109.5000 4.5000e+02 + 4 2 5 2 110.3000 5.2400e+02 + 6 5 24 2 108.5300 4.4300e+02 + 6 5 96 2 108.5300 4.4300e+02 + 5 96 97 2 109.5000 4.5000e+02 + 24 5 96 2 108.5300 4.4300e+02 + 5 24 25 2 109.5000 4.5000e+02 7 8 11 2 109.5000 5.2000e+02 8 7 17 2 109.5000 4.5000e+02 - 7 8 9 2 111.0000 5.3000e+02 7 8 10 2 111.0000 5.3000e+02 - 7 17 96 2 108.5300 4.4300e+02 + 7 8 9 2 111.0000 5.3000e+02 + 7 17 18 2 108.5300 4.4300e+02 + 7 17 60 2 108.5300 4.4300e+02 7 17 14 2 110.3000 5.2400e+02 - 10 8 11 2 110.3000 5.2400e+02 + 9 8 11 2 110.3000 5.2400e+02 9 8 10 2 107.5700 4.8400e+02 - 8 11 78 2 110.3000 5.2400e+02 + 10 8 11 2 110.3000 5.2400e+02 8 11 12 2 110.3000 5.2400e+02 - 9 8 11 2 110.3000 5.2400e+02 - 12 11 78 2 108.5300 4.4300e+02 + 8 11 78 2 110.3000 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1}, {"atom_a": 106, "atom_b": 110, "pair_type": 1}, {"atom_a": 106, "atom_b": 111, "pair_type": 1}, {"atom_a": 106, "atom_b": 109, "pair_type": 1}, {"atom_a": 107, "atom_b": 111, "pair_type": 1}, {"atom_a": 107, "atom_b": 109, "pair_type": 1}, {"atom_a": 107, "atom_b": 110, "pair_type": 1}, {"atom_a": 109, "atom_b": 113, "pair_type": 1}, {"atom_a": 109, "atom_b": 112, "pair_type": 1}, {"atom_a": 109, "atom_b": 114, "pair_type": 1}, {"atom_a": 110, "atom_b": 112, "pair_type": 1}, {"atom_a": 110, "atom_b": 113, "pair_type": 1}, {"atom_a": 110, "atom_b": 114, "pair_type": 1}, {"atom_a": 116, "atom_b": 121, "pair_type": 1}, {"atom_a": 116, "atom_b": 120, "pair_type": 1}, {"atom_a": 118, "atom_b": 121, "pair_type": 1}, {"atom_a": 118, "atom_b": 120, "pair_type": 1}, {"atom_a": 119, "atom_b": 120, "pair_type": 1}, {"atom_a": 119, "atom_b": 121, "pair_type": 1}, {"atom_a": 123, "atom_b": 128, "pair_type": 1}, {"atom_a": 123, "atom_b": 130, "pair_type": 1}, {"atom_a": 123, "atom_b": 129, "pair_type": 1}, {"atom_a": 124, "atom_b": 131, "pair_type": 1}, {"atom_a": 124, "atom_b": 132, "pair_type": 1}, {"atom_a": 124, "atom_b": 133, "pair_type": 1}, {"atom_a": 125, "atom_b": 129, "pair_type": 1}, {"atom_a": 125, "atom_b": 130, "pair_type": 1}, {"atom_a": 125, "atom_b": 128, "pair_type": 1}, {"atom_a": 126, "atom_b": 129, "pair_type": 1}, {"atom_a": 126, "atom_b": 130, "pair_type": 1}, {"atom_a": 126, "atom_b": 128, "pair_type": 1}, {"atom_a": 128, "atom_b": 133, "pair_type": 1}, {"atom_a": 128, "atom_b": 132, "pair_type": 1}, {"atom_a": 128, "atom_b": 131, "pair_type": 1}, {"atom_a": 129, "atom_b": 131, "pair_type": 1}, {"atom_a": 129, "atom_b": 133, "pair_type": 1}, {"atom_a": 129, "atom_b": 132, "pair_type": 1}], "exclusions": [], "preamble": [";----------------------------TITLE -----------------------------------------------------------------------------------------", "; Ethanol", ";", "; This file was generated at 18:19 on 2023-07-31 by", ";", "; Automatic Topology Builder", ";", "; REVISION 2023-06-14 20:38:16", ";---------------------------------------------------------------------------------------------------------------------------", "; Authors : Martin Stroet, Bertrand Caron, Alpeshkumar K. Malde, Thomas Lee, Alan E. Mark", ";", "; Institute : Molecular Dynamics group,", "; School of Chemistry and Molecular Biosciences (SCMB),", "; The University of Queensland, QLD 4072, Australia", "; URL : https://atb.uq.edu.au", "; Citations : 1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, Nair PC, Oostenbrink C, Mark AE.", "; An Automated force field Topology Builder (ATB) and repository: version 1.0.", "; Journal of Chemical Theory and Computation, 2011, 7, 4026-4037.", "; 2. Stroet M, Caron B, Visscher K, Geerke D, Malde AK, Mark AE.", "; Automated Topology Builder version 3.0: Prediction of solvation free enthalpies in water and hexane.", "; DOI:10.1021/acs.jctc.8b00768", ";", "; Disclaimer :", "; While every effort has been made to ensure the accuracy and validity of parameters provided below", "; the assignment of parameters is being based on an automated procedure combining data provided by a", "; given user as well as calculations performed using third party software. They are provided as a guide.", "; The authors of the ATB cannot guarantee that the parameters are complete or that the parameters provided", "; are appropriate for use in any specific application. Users are advised to treat these parameters with discretion", "; and to perform additional validation tests for their specific application if required. Neither the authors", "; of the ATB or The University of Queensland except any responsibly for how the parameters may be used.", ";", "; Release notes and warnings:", "; (1) The topology is based on a set of atomic coordinates and other data provided by the user after", "; after quantum mechanical optimization of the structure using different levels of theory depending on", "; the nature of the molecule.", "; (2) In some cases the automatic bond, bond angle and dihedral type assignment is ambiguous.", "; In these cases alternative type codes are provided at the end of the line.", "; (3) While bonded parameters are taken where possible from the nominated force field non-standard bond, angle and dihedral", "; type code may be incorporated in cases where an exact match could not be found. These are marked as \"non-standard\"", "; or \"uncertain\" in comments.", "; (4) In some cases it is not possible to assign an appropriate parameter automatically. \"%%\" is used as a place holder", "; for those fields that could not be determined automatically. The parameters in these fields must be assigned manually", "; before the file can be used.", ";---------------------------------------------------------------------------------------------------------------------------", "; Input Structure : BWD8", "; Output : ALL ATOM topology", ";\tUse in conjunction with the corresponding all atom PDB file.", ";---------------------------------------------------------------------------------------------------------------------------", "; Citing this topology file", "; ATB molid: 360413", "; ATB Topology Hash: 940bb", ";---------------------------------------------------------------------------------------------------------------------------", "; Final Topology Generation was performed using:", "; A B3LYP/6-31G* optimized geometry.", "; Bonded and van der Waals parameters were taken from the GROMOS 54A7 parameter set.", "; Initial charges were estimated using the ESP method of Merz-Kollman.", "; Final charges and charge groups were generated by method described in the ATB paper.", "; If required, additional bonded parameters were generated from a Hessian matrix calculated at the B3LYP/6-31G* level of theory.", ";---------------------------------------------------------------------------------------------------------------------------", ";", ";"], "moleculetype": {"name": "BWD8", "nrexcl": 3}}, "junctions": []} \ No newline at end of file +{"topology": {"atoms": [{"atom_id": 1, "atom_type": "CPos", "residue_id": 1, "residue_name": "BWD8", "atom_name": "C1", "charge_group_num": 3, "partial_charge": 0.40275, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 2, "atom_type": "HC", "residue_id": 1, "residue_name": "BWD8", "atom_name": "H1", "charge_group_num": 4, "partial_charge": 0.001750000000000005, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 3, "atom_type": "HC", "residue_id": 1, "residue_name": "BWD8", "atom_name": "H2", "charge_group_num": 5, "partial_charge": 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"pair_type": 1}, {"atom_a": 105, "atom_b": 112, "pair_type": 1}, {"atom_a": 106, "atom_b": 110, "pair_type": 1}, {"atom_a": 106, "atom_b": 109, "pair_type": 1}, {"atom_a": 106, "atom_b": 111, "pair_type": 1}, {"atom_a": 107, "atom_b": 110, "pair_type": 1}, {"atom_a": 107, "atom_b": 109, "pair_type": 1}, {"atom_a": 107, "atom_b": 111, "pair_type": 1}, {"atom_a": 109, "atom_b": 112, "pair_type": 1}, {"atom_a": 109, "atom_b": 114, "pair_type": 1}, {"atom_a": 109, "atom_b": 113, "pair_type": 1}, {"atom_a": 110, "atom_b": 112, "pair_type": 1}, {"atom_a": 110, "atom_b": 113, "pair_type": 1}, {"atom_a": 110, "atom_b": 114, "pair_type": 1}, {"atom_a": 116, "atom_b": 121, "pair_type": 1}, {"atom_a": 116, "atom_b": 120, "pair_type": 1}, {"atom_a": 118, "atom_b": 120, "pair_type": 1}, {"atom_a": 118, "atom_b": 121, "pair_type": 1}, {"atom_a": 119, "atom_b": 121, "pair_type": 1}, {"atom_a": 119, "atom_b": 120, "pair_type": 1}, {"atom_a": 123, "atom_b": 130, "pair_type": 1}, {"atom_a": 123, "atom_b": 128, "pair_type": 1}, {"atom_a": 123, "atom_b": 129, "pair_type": 1}, {"atom_a": 124, "atom_b": 133, "pair_type": 1}, {"atom_a": 124, "atom_b": 131, "pair_type": 1}, {"atom_a": 124, "atom_b": 132, "pair_type": 1}, {"atom_a": 125, "atom_b": 129, "pair_type": 1}, {"atom_a": 125, "atom_b": 130, "pair_type": 1}, {"atom_a": 125, "atom_b": 128, "pair_type": 1}, {"atom_a": 126, "atom_b": 130, "pair_type": 1}, {"atom_a": 126, "atom_b": 128, "pair_type": 1}, {"atom_a": 126, "atom_b": 129, "pair_type": 1}, {"atom_a": 128, "atom_b": 133, "pair_type": 1}, {"atom_a": 128, "atom_b": 131, "pair_type": 1}, {"atom_a": 128, "atom_b": 132, "pair_type": 1}, {"atom_a": 129, "atom_b": 131, "pair_type": 1}, {"atom_a": 129, "atom_b": 132, "pair_type": 1}, {"atom_a": 129, "atom_b": 133, "pair_type": 1}], "exclusions": [], "preamble": [";----------------------------TITLE -----------------------------------------------------------------------------------------", "; Ethanol", ";", "; This file was generated at 18:19 on 2023-07-31 by", ";", "; Automatic Topology Builder", ";", "; REVISION 2023-06-14 20:38:16", ";---------------------------------------------------------------------------------------------------------------------------", "; Authors : Martin Stroet, Bertrand Caron, Alpeshkumar K. Malde, Thomas Lee, Alan E. Mark", ";", "; Institute : Molecular Dynamics group,", "; School of Chemistry and Molecular Biosciences (SCMB),", "; The University of Queensland, QLD 4072, Australia", "; URL : https://atb.uq.edu.au", "; Citations : 1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, Nair PC, Oostenbrink C, Mark AE.", "; An Automated force field Topology Builder (ATB) and repository: version 1.0.", "; Journal of Chemical Theory and Computation, 2011, 7, 4026-4037.", "; 2. Stroet M, Caron B, Visscher K, Geerke D, Malde AK, Mark AE.", "; Automated Topology Builder version 3.0: Prediction of solvation free enthalpies in water and hexane.", "; DOI:10.1021/acs.jctc.8b00768", ";", "; Disclaimer :", "; While every effort has been made to ensure the accuracy and validity of parameters provided below", "; the assignment of parameters is being based on an automated procedure combining data provided by a", "; given user as well as calculations performed using third party software. They are provided as a guide.", "; The authors of the ATB cannot guarantee that the parameters are complete or that the parameters provided", "; are appropriate for use in any specific application. Users are advised to treat these parameters with discretion", "; and to perform additional validation tests for their specific application if required. Neither the authors", "; of the ATB or The University of Queensland except any responsibly for how the parameters may be used.", ";", "; Release notes and warnings:", "; (1) The topology is based on a set of atomic coordinates and other data provided by the user after", "; after quantum mechanical optimization of the structure using different levels of theory depending on", "; the nature of the molecule.", "; (2) In some cases the automatic bond, bond angle and dihedral type assignment is ambiguous.", "; In these cases alternative type codes are provided at the end of the line.", "; (3) While bonded parameters are taken where possible from the nominated force field non-standard bond, angle and dihedral", "; type code may be incorporated in cases where an exact match could not be found. These are marked as \"non-standard\"", "; or \"uncertain\" in comments.", "; (4) In some cases it is not possible to assign an appropriate parameter automatically. \"%%\" is used as a place holder", "; for those fields that could not be determined automatically. The parameters in these fields must be assigned manually", "; before the file can be used.", ";---------------------------------------------------------------------------------------------------------------------------", "; Input Structure : BWD8", "; Output : ALL ATOM topology", ";\tUse in conjunction with the corresponding all atom PDB file.", ";---------------------------------------------------------------------------------------------------------------------------", "; Citing this topology file", "; ATB molid: 360413", "; ATB Topology Hash: 940bb", ";---------------------------------------------------------------------------------------------------------------------------", "; Final Topology Generation was performed using:", "; A B3LYP/6-31G* optimized geometry.", "; Bonded and van der Waals parameters were taken from the GROMOS 54A7 parameter set.", "; Initial charges were estimated using the ESP method of Merz-Kollman.", "; Final charges and charge groups were generated by method described in the ATB paper.", "; If required, additional bonded parameters were generated from a Hessian matrix calculated at the B3LYP/6-31G* level of theory.", ";---------------------------------------------------------------------------------------------------------------------------", ";", ";"], "moleculetype": {"name": "BWD8", "nrexcl": 3}}, "junctions": []} \ No newline at end of file diff --git a/data_paper_examples/six_arm_star_monomer_build.png b/data_paper_examples/six_arm_star_monomer_build.png index 2234c91..e3fc6db 100644 Binary files a/data_paper_examples/six_arm_star_monomer_build.png and b/data_paper_examples/six_arm_star_monomer_build.png differ diff --git a/polytop/polytop/Angles.py b/polytop/polytop/Angles.py index f206e5e..2285814 100644 --- a/polytop/polytop/Angles.py +++ b/polytop/polytop/Angles.py @@ -26,7 +26,8 @@ class Angle: B and atoms B and C """ def __init__(self, atom_a: Atom, atom_b: Atom, atom_c: Atom, - angle_type: int, angle_value: float, force_constant: float) -> None: + angle_type: int, angle_value: float, force_constant: float, + format: str = "gromos") -> None: """ Represents an angle between three atoms in a molecular system. @@ -42,6 +43,9 @@ def __init__(self, atom_a: Atom, atom_b: Atom, atom_c: Atom, :type angle_value: float :param force_constant: The force constant associated with the angle. :type force_constant: float + :param format: The forcefield the ITP file is formatted as, options are + "gromos", "amber", "opls" and "charmm" + :type format: str, defaults to "gromos" for GROMOS forcefields. :raises ValueError: If there are not bonds present between atoms A and B and atoms B and C """ @@ -56,20 +60,40 @@ def __init__(self, atom_a: Atom, atom_b: Atom, atom_c: Atom, self.bond_ab, self.bond_bc = Angle.find_bonds(atom_a, atom_b, atom_c) if self.bond_ab is None or self.bond_bc is None: raise ValueError(f"Could not find bonds for angle: {self}") + self.bond_ab.angles.add(self) self.bond_bc.angles.add(self) self.dihedrals = set() + self.format = format @classmethod - def from_line(cls, line: str, atoms): + def from_line(cls, line: str, atoms, format: str = "gromos") -> Angle: + """ + Class method to construct Angle from the line of an ITP file and a + list of all Atom's present in the topology. + + :param line: the ITP file line + :type line: str + :param atoms: list of all Atoms in the Topology + :type atoms: List[Atom] + :param format: The forcefield the ITP file is formatted as, options are + "gromos", "amber", "opls" and "charmm" + :type format: str, defaults to "gromos" for GROMOS forcefields. + :return: the new Angle + :rtype: Angle + """ parts = line.split() atom_a = atoms[int(parts[0]) - 1] atom_b = atoms[int(parts[1]) - 1] atom_c = atoms[int(parts[2]) - 1] angle_type = int(parts[3]) - angle_value = float(parts[4]) - force_constant = float(parts[5]) - return cls(atom_a, atom_b, atom_c, angle_type, angle_value, force_constant) + if format=="charmm": + angle_value = None + force_constant = None + else: + angle_value = float(parts[4]) + force_constant = float(parts[5]) + return cls(atom_a, atom_b, atom_c, angle_type, angle_value, force_constant, format) @staticmethod def find_bonds(atom_a: Atom, atom_b: Atom, atom_c: Atom): @@ -111,11 +135,11 @@ def clone_angle_changing(self, from_atom: Atom, to_atom: Atom) -> Angle: :rtype: Angle """ if self.atom_a == from_atom: # first atom is being replaced - new_angle = Angle(to_atom, self.atom_b, self.atom_c, self.angle_type, self.angle_value, self.force_constant) + new_angle = Angle(to_atom, self.atom_b, self.atom_c, self.angle_type, self.angle_value, self.force_constant, self.format) elif self.atom_b == from_atom: # second atom is being replaced - new_angle = Angle(self.atom_a, to_atom, self.atom_c, self.angle_type, self.angle_value, self.force_constant) + new_angle = Angle(self.atom_a, to_atom, self.atom_c, self.angle_type, self.angle_value, self.force_constant, self.format) elif self.atom_c == from_atom: # third atom is being replaced - new_angle = Angle(self.atom_a, self.atom_b, to_atom, self.angle_type, self.angle_value, self.force_constant) + new_angle = Angle(self.atom_a, self.atom_b, to_atom, self.angle_type, self.angle_value, self.force_constant, self.format) else: raise ValueError(f"Atom {from_atom} is not in angle {self}") return new_angle @@ -151,7 +175,11 @@ def remove(self): self.bond_bc.angles.remove(self) def __str__(self): - return f"{self.atom_a.atom_id:>5} {self.atom_b.atom_id:>5} {self.atom_c.atom_id:>5} {self.angle_type:>5} {self.angle_value:>10.4f} {self.force_constant:.4e}" + # TODO: figure out why topology.to_ITP is causing Angles to write as a different format + if self.format == "charmm" or self.angle_value==None and self.force_constant==None: + return f"{self.atom_a.atom_id:>5} {self.atom_b.atom_id:>5} {self.atom_c.atom_id:>5} {self.angle_type:>5}" + else: + return f"{self.atom_a.atom_id:>5} {self.atom_b.atom_id:>5} {self.atom_c.atom_id:>5} {self.angle_type:>5} {self.angle_value:>10.4f} {self.force_constant:.4e}" def __repr__(self) -> str: return f"Angle({self.atom_a.atom_id}, {self.atom_b.atom_id}, {self.atom_c.atom_id})" diff --git a/polytop/polytop/Atoms.py b/polytop/polytop/Atoms.py index d763744..d643467 100644 --- a/polytop/polytop/Atoms.py +++ b/polytop/polytop/Atoms.py @@ -134,7 +134,7 @@ def element(self) -> str: element_name = element_name[0] return element_name - #TO DO: deconvulute following 3 functions, and atom_name, atom_id and index properties... + #TODO: deconvulute following 3 functions, and atom_name, atom_id and index properties... @element.setter def element(self, value: str): """ @@ -266,7 +266,9 @@ def deduplicate_bonds(self): bonds_to_remove = [] for bond in self.bonds: if bond.other_atom(self) in neighbours: - bonds_to_remove.append(bond) + # find duplicate bond and add the one without angles to bonds_to_remove + empty_bond = Bond.from_atoms(self, bond.other_atom(self), find_empty = True) + bonds_to_remove.append(empty_bond) else: neighbours.append(bond.other_atom(self)) for bond in bonds_to_remove: diff --git a/polytop/polytop/Bonds.py b/polytop/polytop/Bonds.py index b6f665d..2c0e4f1 100644 --- a/polytop/polytop/Bonds.py +++ b/polytop/polytop/Bonds.py @@ -28,6 +28,7 @@ def __init__( bond_length: float, force_constant: float, order: int = 1, + format: str = "gromos" ) -> None: """ Represents a bond between two atoms in a molecular system. @@ -44,6 +45,9 @@ def __init__( :type force_constant: float :param order: The bond order, defaults to 1 (single bond) :type order: int, optional + :param format: The forcefield the ITP file is formatted as, options are + "gromos", "amber", "opls" and "charmm" + :type format: str, defaults to "gromos" for GROMOS forcefields. :raises ValueError: if either atom_a or atom_b are None """ if atom_a is None or atom_b is None: @@ -59,9 +63,10 @@ def __init__( atom_b.bonds.add(self) self.order = order self.angles = set() + self.format = format @classmethod - def from_line(cls, line: str, atoms: List["Atom"]) -> Bond: + def from_line(cls, line: str, atoms: List["Atom"], format: str = "gromos") -> Bond: """ Class method to construct Bond from the line of an ITP file and a list of all Atom's present in the topology. @@ -70,6 +75,9 @@ def from_line(cls, line: str, atoms: List["Atom"]) -> Bond: :type line: str :param atoms: list of all Atoms in the Topology :type atoms: List[Atom] + :param format: The forcefield the ITP file is formatted as, options are + "gromos", "amber", "opls" and "charmm" + :type format: str, defaults to "gromos" for GROMOS forcefields. :return: the new Bond :rtype: Bond """ @@ -77,43 +85,52 @@ def from_line(cls, line: str, atoms: List["Atom"]) -> Bond: atom_a = atoms[int(parts[0]) - 1] atom_b = atoms[int(parts[1]) - 1] bond_type = int(parts[2]) - bond_length = float(parts[3]) - force_constant = float(parts[4]) + if format=="charmm": + bond_length = 0 # 0 instead of None enables extend to work, is not saved to output + force_constant = 0 + else: + bond_length = float(parts[3]) + force_constant = float(parts[4]) - return cls(atom_a, atom_b, bond_type, bond_length, force_constant) + return cls(atom_a, atom_b, bond_type, bond_length, force_constant, format=format) @staticmethod - def from_atoms(atom_a: "Atom", atom_b: "Atom") -> Bond: + def from_atoms(atom_a: "Atom", atom_b: "Atom", find_empty: bool = False) -> Bond: """ Class method to find and return Bond from between two Atoms. :param atom_a: The first atom involved in the angle. :type atom_a: Atom - :param atom_b: The central atom in the angle. - :type atom_b: Atom - :param atom_c: The third atom involved in the angle. - :type atom_c: Atom - :return: the new Angle - :rtype: Angle - - :param atom_a: The first atom involved in the bond. - :type atom_a: Atom - :param atom_b: The second atom involved in the bond. + :param atom_b: The second atom in the angle. :type atom_b: Atom + :param find_empty: Optional argument used when de-duplicating bonds to + ensure the bond without angles associated is returned to delete. + :type find_empty: bool, defaults to False :return: a Bond between these Atoms, or None if either atom_a or atom_b are None or there is not a bond between them. :rtype: Bond """ if atom_a is None or atom_b is None: return None - return next( - ( - bond - for bond in atom_a.bonds - if bond.atom_b == atom_b or bond.atom_a == atom_b - ), - None, - ) + + send = list(bond for bond in atom_a.bonds if bond.atom_b == atom_b or bond.atom_a == atom_b) + # need to prevent ambiguity in selecting bonds, so that only one duplicate + # bond created during polymer extension gets all of the Angles and Dihedrals, + # and the other is removed during bond de-duplication + if len(send) > 1 and find_empty==False: + # duplicate bond, return the bond that has angles already to give it more + has_angles = list(bond for bond in send if len(bond.angles)>=1 and bond.angles!=None and bond.angles!=set())[0] + return has_angles + elif len(send) > 1 and find_empty==True: + # duplicate bond, return the bond with no angles to delete + no_angles = list(bond for bond in send if len(bond.angles)==0 or bond.angles==None or bond.angles==set())[0] + return no_angles + elif len(send)==1: + # only 1 bond for this atom pair, return it + return send[0] + else: + # this atom pair does not have a shared bond + return None def contains_atom(self, atom: "Atom") -> bool: """ @@ -142,14 +159,14 @@ def clone_bond_changing(self, from_atom: "Atom", to_atom: "Atom") -> Bond: :rtype: Bond """ if self.atom_a == from_atom: # first atom is being replaced - new_bond = Bond(to_atom, self.atom_b, self.bond_type, self.bond_length, self.force_constant, self.order) + new_bond = Bond(to_atom, self.atom_b, self.bond_type, self.bond_length, self.force_constant, self.order, self.format) elif self.atom_b == from_atom: # second atom is being replaced - new_bond = Bond(self.atom_a, to_atom, self.bond_type, self.bond_length, self.force_constant, self.order) + new_bond = Bond(self.atom_a, to_atom, self.bond_type, self.bond_length, self.force_constant, self.order, self.format) else: raise ValueError(f"Atom {from_atom} is not in bond {self}") return new_bond - def other_atom(self, atom: "Atom")-> Atom: + def other_atom(self, atom: "Atom")-> "Atom": """ Check if the given Atom is in this Angle and return a list of the other atoms present in this Angle (i.e. discluding 'atom'). @@ -218,7 +235,10 @@ def remove(self): self.atom_b.bonds.remove(self) def __str__(self): - return f"{self.atom_a.atom_id:>5} {self.atom_b.atom_id:>5} {self.bond_type:>5} {self.bond_length:>10.4f} {self.force_constant:.4e}" + if self.format == "charmm": + return f"{self.atom_a.atom_id:>5} {self.atom_b.atom_id:>5} {self.bond_type:>5}" + else: + return f"{self.atom_a.atom_id:>5} {self.atom_b.atom_id:>5} {self.bond_type:>5} {self.bond_length:>10.4f} {self.force_constant:.4e}" def __repr__(self) -> str: if self.order == 1: diff --git a/polytop/polytop/Dihedrals.py b/polytop/polytop/Dihedrals.py index 933587a..1acafc9 100644 --- a/polytop/polytop/Dihedrals.py +++ b/polytop/polytop/Dihedrals.py @@ -3,15 +3,31 @@ import warnings from enum import IntEnum from typing import Dict, List, Union +# import pdb +# pdb.set_trace() from .Angles import Angle class Dihedral_type(IntEnum): """ Enum to track Dihedral types including proper (1) and improper (2). + + Proper dihedrals also include: Ryckaert-Bellemans (3), Fourier (5), + proper (multiple) (9), tabulated (8) and restricted (10). + Improper dihedrals also include: periodic improper (4). + + For more information, see + `GROMACS documentation ` + and view Table 14. """ proper = 1 improper = 2 + ryckaert_bellemans = 3 + periodic_improper = 4 + fourier = 5 + multiple = 9 + tabulated = 8 + restricted = 10 # TODO: add additional dihedral types here # but remember to update the constraint properties @@ -27,10 +43,26 @@ def is_rotational_constraint(self) -> bool: :return: True if this Dihedral is proper, and False if not. :rtype: bool """ - return self in [Dihedral_type.proper] + return self in [Dihedral_type.proper, Dihedral_type.multiple, + Dihedral_type.tabulated, Dihedral_type.restricted] @property - def is_planar_constraint(self) -> bool: # + def is_rotational_constraint_with_constants(self) -> bool: + """ + Proper dihedral: constrains torsional rotation around the BC bond, but + is defined with 6 constants increase of degrees, energy and multiplicity. + + | A -◟B | + | / | + | C◝- D | + + :return: True if this Dihedral is proper with constants, and False if not. + :rtype: bool + """ + return self in [Dihedral_type.ryckaert_bellemans, Dihedral_type.fourier] + + @property + def is_planar_constraint(self) -> bool: """ Improper dihedral: constrains orientation of D WRT the CAB plane. In other words, the two angles are B-A-C and B-A-D @@ -43,6 +75,21 @@ def is_planar_constraint(self) -> bool: # :rtype: bool """ return self in [Dihedral_type.improper] + + @property + def is_periodic_planar_constraint(self) -> bool: + """ + Improper dihedral: constrains orientation of D WRT the CAB plane. In + other words, the two angles are B-A-C and B-A-D + + | B | + | | | + | C -◜A◝ - D | + + :return: True if this Dihedral is periodic improper, and False if not. + :rtype: bool + """ + return self in [Dihedral_type.periodic_improper] class Dihedral: """ @@ -74,9 +121,11 @@ def __init__( atom_c: "Atom", atom_d: "Atom", dihedral_type: Dihedral_type, - phase_angle: float, - force_constant: float, - multiplicity: int, + phase_angle: float = None, + force_constant: float = None, + multiplicity: int = None, + constants: list[float] = None, + format: str = "gromos", ) -> None: """ Represents a dihedral angle formed by four atoms in a molecular system. @@ -97,6 +146,12 @@ def __init__( :type force_constant: float :param multiplicity: The multiplicity of the dihedral angle. :type multiplicity: int + :param constants: The constants used to describe the dihedra + Ryckaert-Bellemans or Fourier potential. + :type constants: list[int] + :param format: The forcefield the ITP file is formatted as, options are + "gromos", "amber", "opls" and "charmm" + :type format: str, defaults to "gromos" for GROMOS forcefields. :raises ValueError: If unable to find an Angle for the Dihedral. :raises ValueError: If an unknown Dihedral_type is provided. """ @@ -108,33 +163,126 @@ def __init__( self.phase_angle = phase_angle self.force_constant = force_constant self.multiplicity = multiplicity - if self.dihedral_type.is_rotational_constraint: - if angle_abc := Angle.from_atoms(atom_a, atom_b, atom_c): - angle_abc.dihedrals.add(self) - self.angle_a = angle_abc + self.constants = constants + self.format = format + # angles and bonds for OPLS forcefield atom order + if self.format == "opls": + if self.dihedral_type.is_rotational_constraint or self.dihedral_type.is_rotational_constraint_with_constants: + if angle_abc := Angle.from_atoms(atom_a, atom_b, atom_c): + angle_abc.dihedrals.add(self) + self.angle_a = angle_abc + else: + raise ValueError(f"Could not find angle for dihedral: {self}") + if angle_bcd := Angle.from_atoms(atom_b, atom_c, atom_d): + angle_bcd.dihedrals.add(self) + self.angle_b = angle_bcd + else: + raise ValueError(f"Could not find angle for dihedral: {self}") + elif self.dihedral_type.is_planar_constraint or self.dihedral_type.is_periodic_planar_constraint: + if angle_abc := Angle.from_atoms(atom_a, atom_b, atom_c): + angle_abc.dihedrals.add(self) + self.angle_a = angle_abc + else: + raise ValueError(f"Could not find angle for dihedral: {self}") + if angle_abd := Angle.from_atoms(atom_a, atom_b, atom_d): + angle_abd.dihedrals.add(self) + self.angle_b = angle_abd + else: + raise ValueError(f"Could not find angle for dihedral: {self}") else: - raise ValueError(f"Could not find angle for dihedral: {self}") - if angle_bcd := Angle.from_atoms(atom_b, atom_c, atom_d): - angle_bcd.dihedrals.add(self) - self.angle_b = angle_bcd + raise ValueError(f"Unknown dihedral type: {dihedral_type}") + + # angles and bonds for GROMOS and CHARMM forcefield atom orders + if self.format == "gromos" or self.format == "charmm": + if self.dihedral_type.is_rotational_constraint or self.dihedral_type.is_rotational_constraint_with_constants: + if angle_abc := Angle.from_atoms(atom_a, atom_b, atom_c): + angle_abc.dihedrals.add(self) + self.angle_a = angle_abc + else: + raise ValueError(f"Could not find angle for dihedral: {self}") + if angle_bcd := Angle.from_atoms(atom_b, atom_c, atom_d): + angle_bcd.dihedrals.add(self) + self.angle_b = angle_bcd + else: + raise ValueError(f"Could not find angle for dihedral: {self}") + elif self.dihedral_type.is_planar_constraint or self.dihedral_type.is_periodic_planar_constraint: + if angle_bac := Angle.from_atoms(atom_b, atom_a, atom_c): + angle_bac.dihedrals.add(self) + self.angle_a = angle_bac + else: + raise ValueError(f"Could not find angle for dihedral: {self}") + if angle_bad := Angle.from_atoms(atom_b, atom_a, atom_d): + angle_bad.dihedrals.add(self) + self.angle_b = angle_bad + else: + raise ValueError(f"Could not find angle for dihedral: {self}") else: - raise ValueError(f"Could not find angle for dihedral: {self}") - elif self.dihedral_type.is_planar_constraint: - if angle_bac := Angle.from_atoms(atom_b, atom_a, atom_c): - angle_bac.dihedrals.add(self) - self.angle_a = angle_bac - else: - raise ValueError(f"Could not find angle for dihedral: {self}") - if angle_bad := Angle.from_atoms(atom_b, atom_a, atom_d): - angle_bad.dihedrals.add(self) - self.angle_b = angle_bad + raise ValueError(f"Unknown dihedral type: {dihedral_type}") + + # angles and bonds for AMBER forcefield atom order + if self.format == "amber": + if self.dihedral_type.is_periodic_planar_constraint: + if angle_bac := Angle.from_atoms(atom_a, atom_b, atom_c): + angle_bac.dihedrals.add(self) + self.angle_a = angle_bac + else: # could not resolve angles, shuffle and retry + if self.phase_angle == 180 and self.multiplicity == 2: + warnings.warn(f"Could not find angle for dihedral: {self}," + f" swapping the order of atom {self.atom_b.atom_name} and" + f" atom {self.atom_c.atom_name} and retrying. The phase angle" + " is 180 and the multiplicity is 2, so the" + " dihedral parameters will not be impacted.") + if angle_bac := Angle.from_atoms(atom_a, atom_c, atom_b): + angle_bac.dihedrals.add(self) + self.angle_a = angle_bac + else: + raise ValueError(f"Could not find angle for dihedral: {self}") + else: + raise ValueError(f"Could not find angle for dihedral: {self}") + if angle_bad := Angle.from_atoms(atom_a, atom_b, atom_d): + angle_bad.dihedrals.add(self) + self.angle_b = angle_bad + else: # could not resolve angles, shuffle and retry + if self.phase_angle == 180 and self.multiplicity == 2: + warnings.warn(f"Could not find angle for dihedral: {self}," + f" swapping the order of atom {self.atom_b.atom_name} and" + f" atom {self.atom_c.atom_name} and retrying. The phase angle" + " is 180 and the multiplicity is 2, so the" + " dihedral parameters will not be impacted.") + if angle_bad := Angle.from_atoms(atom_a, atom_c, atom_d): + angle_bad.dihedrals.add(self) + self.angle_b = angle_bad + else: + raise ValueError(f"Could not find angle for dihedral: {self}") + else: + raise ValueError(f"Could not find angle for dihedral: {self}") + elif self.dihedral_type.is_rotational_constraint or self.dihedral_type.is_rotational_constraint_with_constants: + if angle_abc := Angle.from_atoms(atom_a, atom_b, atom_c): + angle_abc.dihedrals.add(self) + self.angle_a = angle_abc + else: + raise ValueError(f"Could not find angle for dihedral: {self}") + if angle_bcd := Angle.from_atoms(atom_b, atom_c, atom_d): + angle_bcd.dihedrals.add(self) + self.angle_b = angle_bcd + else: + raise ValueError(f"Could not find angle for dihedral: {self}") + elif self.dihedral_type.is_planar_constraint: + if angle_bac := Angle.from_atoms(atom_a, atom_b, atom_c): + angle_bac.dihedrals.add(self) + self.angle_a = angle_bac + else: + raise ValueError(f"Could not find angle for dihedral: {self}") + if angle_bad := Angle.from_atoms(atom_a, atom_b, atom_d): + angle_bad.dihedrals.add(self) + self.angle_b = angle_bad + else: + raise ValueError(f"Could not find angle for dihedral: {self}") else: - raise ValueError(f"Could not find angle for dihedral: {self}") - else: - raise ValueError(f"Unknown dihedral type: {dihedral_type}") + raise ValueError(f"Unknown dihedral type: {dihedral_type}") @classmethod - def from_line(cls, line: str, atoms) -> Dihedral: + def from_line(cls, line: str, atoms, format: str = "gromos") -> Dihedral: """ Class method to construct Dihedral from the line of an ITP file and a list of all Atom's present in the topology. @@ -143,6 +291,9 @@ def from_line(cls, line: str, atoms) -> Dihedral: :type line: str :param atoms: list of all Atoms in the Topology :type atoms: List[Atom] + :param format: The forcefield the ITP file is formatted as, options are + "gromos", "amber", "opls" and "charmm" + :type format: str, defaults to "gromos" for GROMOS forcefields. :return: the new Dihedral :rtype: Dihedral """ @@ -152,15 +303,28 @@ def from_line(cls, line: str, atoms) -> Dihedral: atom_c = atoms[int(parts[2]) - 1] atom_d = atoms[int(parts[3]) - 1] dihedral_type = Dihedral_type(int(parts[4])) - phase_angle = float(parts[5]) - force_constant = float(parts[6]) - if dihedral_type.is_rotational_constraint: + if format=="charmm": + phase_angle = None + force_constant = None + else: + phase_angle = float(parts[5]) + force_constant = float(parts[6]) + constants = [] + if format!="charmm" and (dihedral_type.is_rotational_constraint or dihedral_type.is_periodic_planar_constraint): multiplicity = int(parts[7]) - elif dihedral_type.is_planar_constraint: + elif dihedral_type.is_planar_constraint or dihedral_type.is_rotational_constraint_with_constants or format=="charmm": multiplicity = None # multiplicity is not required for improper dihedrals else: warnings.warn(f"Unknown dihedral type: {dihedral_type}") + if dihedral_type.is_rotational_constraint_with_constants: + constants = [float(parts[5]), float(parts[6]), float(parts[7]), float(parts[8]), float(parts[9])] + if len(parts) > 10: # only append sixth constant if available (in Rychaert-Bellemans, but not in Fourier dihedral type) + constants.append(float(parts[10])) + # set angle and force to None + phase_angle = None + force_constant = None + return cls( atom_a, atom_b, @@ -170,6 +334,8 @@ def from_line(cls, line: str, atoms) -> Dihedral: phase_angle, force_constant, multiplicity, + constants, + format ) @staticmethod @@ -178,18 +344,11 @@ def find_angles( atom_b: "Atom", atom_c: "Atom", atom_d: "Atom", + format: str = "gromos", ) -> tuple[Angle|None, Angle|None]: """ Class method to find Angles present in this Dihedral. - :param atom_a: The first atom involved in the angle. - :type atom_a: Atom - :param atom_b: The central atom in the angle. - :type atom_b: Atom - :param atom_c: The third atom involved in the angle. - :type atom_c: Atom - - :param atom_a: The first atom involved in the Dihedral. :type atom_a: Atom :param atom_b: The second atom involved in the Dihedral. @@ -198,15 +357,31 @@ def find_angles( :type atom_c: Atom :param atom_d: The fourth atom involved in the Dihedral. :type atom_d: Atom + :param format: The forcefield the ITP file is formatted as, options are + "gromos", "amber", "opls" and "charmm" + :type format: str, defaults to "gromos" for GROMOS forcefields. :return: a tuple containing the two Angles involved in this Dihedral :rtype: tuple[Angle, Angle] or tuple[None, None] if dihedral type is neither proper or improper """ - angle_abc = Angle.from_atoms(atom_a, atom_b, atom_c) - angle_bcd = Angle.from_atoms(atom_b, atom_c, atom_d) + if format=="gromos" or format=="charmm": + angle_abc = Angle.from_atoms(atom_a, atom_b, atom_c) + angle_bcd = Angle.from_atoms(atom_b, atom_c, atom_d) + + angle_bac = Angle.from_atoms(atom_b, atom_a, atom_c) + angle_bad = Angle.from_atoms(atom_b, atom_a, atom_d) + elif format == "opls": + angle_abc = Angle.from_atoms(atom_a, atom_b, atom_c) + angle_bcd = Angle.from_atoms(atom_b, atom_c, atom_d) + + angle_bac = Angle.from_atoms(atom_a, atom_b, atom_c) + angle_bad = Angle.from_atoms(atom_a, atom_b, atom_d) + else: # format == "amber" + angle_abc = Angle.from_atoms(atom_a, atom_b, atom_c) + angle_bcd = Angle.from_atoms(atom_b, atom_c, atom_d) - angle_bac = Angle.from_atoms(atom_b, atom_a, atom_c) - angle_bad = Angle.from_atoms(atom_b, atom_a, atom_d) + angle_bac = Angle.from_atoms(atom_b, atom_a, atom_c) + angle_bad = Angle.from_atoms(atom_b, atom_a, atom_d) if ( angle_abc and angle_bcd and angle_abc.dihedrals & angle_bcd.dihedrals @@ -263,6 +438,7 @@ def from_atoms( atom_b: "Atom", atom_c: "Atom", atom_d: "Atom", + format: str = "gromos" ) -> Dihedral: """ Class method to construct Dihedral from four Atoms. There must be at @@ -277,11 +453,14 @@ def from_atoms( :type atom_c: Atom :param atom_d: The fourth atom involved in the Dihedral :type atom_d: Atom + :param format: The forcefield the ITP file is formatted as, options are + "gromos", "amber", "opls" and "charmm" + :type format: str, defaults to "gromos" for GROMOS forcefields. :return: the new Dihedral, or None if the Dihedral_type is neither proper or improper :rtype: Dihedral """ - angle_a, angle_b = Dihedral.find_angles(atom_a, atom_b, atom_c, atom_d) + angle_a, angle_b = Dihedral.find_angles(atom_a, atom_b, atom_c, atom_d, format) if angle_a is None or angle_b is None: return None common_dihedrals = angle_a.dihedrals & angle_b.dihedrals @@ -303,22 +482,26 @@ def clone_dihedral_changing(self, from_atom: "Atom", to_atom: "Atom") -> Dihedra :rtype: Dihedral """ if self.atom_a == from_atom: - new_dihedral = Dihedral(to_atom, self.atom_b, self.atom_c, self.atom_d, self.dihedral_type, self.phase_angle, self.force_constant, self.multiplicity) + new_dihedral = Dihedral(to_atom, self.atom_b, self.atom_c, self.atom_d, self.dihedral_type, self.phase_angle, self.force_constant, self.multiplicity, self.constants, self.format) elif self.atom_b == from_atom: - new_dihedral = Dihedral(self.atom_a, to_atom, self.atom_c, self.atom_d, self.dihedral_type, self.phase_angle, self.force_constant, self.multiplicity) + new_dihedral = Dihedral(self.atom_a, to_atom, self.atom_c, self.atom_d, self.dihedral_type, self.phase_angle, self.force_constant, self.multiplicity, self.constants, self.format) elif self.atom_c == from_atom: - new_dihedral = Dihedral(self.atom_a, self.atom_b, to_atom, self.atom_d, self.dihedral_type, self.phase_angle, self.force_constant, self.multiplicity) + new_dihedral = Dihedral(self.atom_a, self.atom_b, to_atom, self.atom_d, self.dihedral_type, self.phase_angle, self.force_constant, self.multiplicity, self.constants, self.format) elif self.atom_d == from_atom: - new_dihedral = Dihedral(self.atom_a, self.atom_b, self.atom_c, to_atom, self.dihedral_type, self.phase_angle, self.force_constant, self.multiplicity) + new_dihedral = Dihedral(self.atom_a, self.atom_b, self.atom_c, to_atom, self.dihedral_type, self.phase_angle, self.force_constant, self.multiplicity, self.constants, self.format) else: raise ValueError(f"Atom {from_atom} is not in dihedral {self}") return new_dihedral def __str__(self): - if self.dihedral_type.is_rotational_constraint: + if self.format == "charmm": + return f"{self.atom_a.atom_id:>5} {self.atom_b.atom_id:>5} {self.atom_c.atom_id:>5} {self.atom_d.atom_id:>5} {self.dihedral_type:>5}" + elif self.dihedral_type.is_rotational_constraint or self.dihedral_type.is_periodic_planar_constraint: return f"{self.atom_a.atom_id:>5} {self.atom_b.atom_id:>5} {self.atom_c.atom_id:>5} {self.atom_d.atom_id:>5} {self.dihedral_type:>5} {self.phase_angle:>10.4f} {self.force_constant:.4e} {self.multiplicity:>5}" elif self.dihedral_type.is_planar_constraint: return f"{self.atom_a.atom_id:>5} {self.atom_b.atom_id:>5} {self.atom_c.atom_id:>5} {self.atom_d.atom_id:>5} {self.dihedral_type:>5} {self.phase_angle:>10.4f} {self.force_constant:.4e}" + elif self.dihedral_type.is_rotational_constraint_with_constants: + return f"{self.atom_a.atom_id:>5} {self.atom_b.atom_id:>5} {self.atom_c.atom_id:>5} {self.atom_d.atom_id:>5} {self.dihedral_type:>5} {self.constants[0]:>10.3f} {self.constants[1]:>10.3f} {self.constants[2]:>10.3f} {self.constants[3]:>10.3f} {self.constants[4]:>10.3f} {self.constants[5]:>10.3f}" def __repr__(self) -> str: return f"Dihedral({self.atom_a.atom_id}, {self.atom_b.atom_id}, {self.atom_c.atom_id}, {self.atom_d.atom_id})" @@ -335,7 +518,8 @@ def to_dict(self) -> dict: 'dihedral_type': self.dihedral_type, 'phase_angle': self.phase_angle, 'force_constant': self.force_constant, - 'multiplicity': self.multiplicity} + 'multiplicity': self.multiplicity, + 'constants' = self.constants} :return: a dictionary containing the id's of its Atoms and other attributes of this Dihedral. @@ -350,10 +534,11 @@ def to_dict(self) -> dict: 'phase_angle': self.phase_angle, 'force_constant': self.force_constant, 'multiplicity': self.multiplicity, + 'constants': self.constants, } @classmethod - def from_dict(cls, data: Dict[str, Union[int, float]], atoms: List["Atom"]) -> Dihedral: + def from_dict(cls, data: Dict[str, Union[int, float]], atoms: List["Atom"], format: str = "gromos") -> Dihedral: """ Create a new Dihedral from a dictionary (such as that created with Dihedral.to_dict()) and list of Atoms. Will retrieve an existing @@ -367,7 +552,8 @@ def from_dict(cls, data: Dict[str, Union[int, float]], atoms: List["Atom"]) -> D 'dihedral_type': self.dihedral_type, 'phase_angle': self.phase_angle, 'force_constant': self.force_constant, - 'multiplicity': self.multiplicity} + 'multiplicity': self.multiplicity, + 'constants' = self.constants} :param data: dictionary containing data to make a Dihedral, generate with 'to_dict()'. @@ -376,6 +562,9 @@ def from_dict(cls, data: Dict[str, Union[int, float]], atoms: List["Atom"]) -> D long as the id's of the four atoms specified in the data dict are present. :type atoms: List[Atom] + :param format: The forcefield the ITP file is formatted as, options are + "gromos", "amber", "opls" and "charmm" + :type format: str, defaults to "gromos" for GROMOS forcefields. :return: a new Dihedral :rtype: Dihedral """ @@ -384,7 +573,7 @@ def from_dict(cls, data: Dict[str, Union[int, float]], atoms: List["Atom"]) -> D atom_c = next((atom for atom in atoms if atom.atom_id == data['atom_c']), None) atom_d = next((atom for atom in atoms if atom.atom_id == data['atom_d']), None) # check for existing dihedrals - dihedral = Dihedral.from_atoms(atom_a, atom_b, atom_c, atom_d) + dihedral = Dihedral.from_atoms(atom_a, atom_b, atom_c, atom_d, format=format) if dihedral is not None: return dihedral else: @@ -392,5 +581,7 @@ def from_dict(cls, data: Dict[str, Union[int, float]], atoms: List["Atom"]) -> D dihedral_type = data['dihedral_type'], phase_angle = data['phase_angle'], force_constant = data['force_constant'], - multiplicity = data['multiplicity']) + multiplicity = data['multiplicity'], + constants = data['constants'], + format = format) diff --git a/polytop/polytop/Polymer.py b/polytop/polytop/Polymer.py index 9583c21..df5b674 100644 --- a/polytop/polytop/Polymer.py +++ b/polytop/polytop/Polymer.py @@ -186,6 +186,11 @@ def extend(self, monomer, from_junction_name: str, to_junction_name: str, keep_c Dihedrals are correct. For best results: + * Do NOT extend a Polymer of a given format (e.g. gromos), with a + Monomer of a different format (e.g. AMBER). This is not recommended as + it is not the supported functionality and has NOT been tested. PolyTop + may crash, produce an incorrect Polymer Topology or behave in an + undefined manner. * Provide topologies where all atoms that will be lost have a partial charge of 0. This will ensure the charge of each atom in the resulting Polymer is identical to it's charge in the provided Monomer it came from. diff --git a/polytop/polytop/Topology.py b/polytop/polytop/Topology.py index 07602a2..0b99669 100644 --- a/polytop/polytop/Topology.py +++ b/polytop/polytop/Topology.py @@ -51,6 +51,7 @@ def __init__( atoms: Optional[List[Atom]] = None, preamble: Optional[List[str]] = None, molecule_type: Optional[MoleculeType] = None, + format: str = "gromos", ): """ Represents the topology of a molecular system, including atoms, bonds, @@ -64,6 +65,9 @@ def __init__( :param molecule_type: the type of molecule represented by the topology, defaults to None :type molecule_type: Optional[MoleculeType], optional + :param format: The forcefield the ITP file is formatted as, options are + "gromos", "amber", "opls" and "charmm" + :type format: str, defaults to "gromos" for GROMOS forcefields. """ self.molecule_type = molecule_type self.atoms = atoms or [] @@ -71,6 +75,7 @@ def __init__( self.title = "Unknown molecule" if self.preamble and self.preamble[1].startswith(';'): self.title = self.preamble[1].lstrip('; ') + self.format = format def copy(self) -> Topology: """ @@ -94,11 +99,12 @@ def copy(self) -> Topology: for angle in self.angles: Angle.from_dict(angle.to_dict(),new_atoms) for dihedral in self.dihedrals: - Dihedral.from_dict(dihedral.to_dict(),new_atoms) + Dihedral.from_dict(dihedral.to_dict(),new_atoms,format=self.format) new_topology = Topology( atoms=new_atoms, preamble=self.preamble.copy(), - molecule_type=copy.copy(self.molecule_type) + molecule_type=copy.copy(self.molecule_type), + format=self.format, ) return new_topology @@ -259,22 +265,28 @@ def _rearrange_atoms(self): return atoms @classmethod - def from_ITP(cls, file_path: str, preprocess=None) -> Topology: + def from_ITP(cls, file_path: str, preprocess=None, format: str = "gromos") -> Topology: """ - Class method to create a Topology object from a GROMACS ITP file. + Class method to create a Topology object from an ITP file. Note: this function does not explicitly check that moleculetype.nrexcl = number of exclusions associated with atoms. - :param file_path: the path to the GROMACS ITP file. + :param file_path: the path to the GROMOS ITP file. :type file_path: str :param preprocess: function to preprocess the topology, that must accept the section and line as arguments in that order, defaults to None. :type preprocess: lambda function, optional + :param format: The forcefield the ITP file is formatted as, options are + "gromos", "amber", "opls" and "charmm" + :type format: str, defaults to "gromos" for GROMOS forcefields. :return: the created Topology object. :rtype: Topology """ + if format not in ["gromos", "charmm", "amber", "opls"]: + raise ValueError("Invalid format! Provide 'gromos', 'charmm', 'amber' or 'opls'\ + - note 'gromos' is default if format string is not provided") with open(file_path, "r") as f: lines = f.readlines() @@ -292,6 +304,9 @@ def from_ITP(cls, file_path: str, preprocess=None) -> Topology: continue if line.startswith("["): section = line.strip("[] ").lower() + if section.__contains__(";"): # cleanup and remove comments if present + cut = section.split(";")[0] + section = cut.strip("[] ") continue if preprocess is not None: line = preprocess(section, line) @@ -304,13 +319,13 @@ def from_ITP(cls, file_path: str, preprocess=None) -> Topology: atom.element atoms.append(atom) elif section == "bonds": - Bond.from_line(line, atoms) + Bond.from_line(line, atoms, format=format) elif section == "angles": - Angle.from_line(line, atoms) + Angle.from_line(line, atoms, format=format) elif section == "pairs": Pair.from_line(line, atoms) elif section == "dihedrals": - Dihedral.from_line(line, atoms) + Dihedral.from_line(line, atoms, format=format) elif section == "exclusions": if len(line.split()) > 2: for second_atom in range(1, len(line.split())): @@ -320,11 +335,11 @@ def from_ITP(cls, file_path: str, preprocess=None) -> Topology: Exclusion.from_line(line, atoms) else: warnings.warn(f"Unknown section {section} in {file_path}") - return cls(atoms, preamble, molecule_type) + return cls(atoms, preamble, molecule_type, format) def to_ITP(self, file_path: str): """ - Write the Topology to a GROMACS ITP file. + Write the Topology to a GROMACS ITP file of the desired forcefield format. :param file_path: the path to and the desired name of the GROMACS ITP file. @@ -341,9 +356,10 @@ def to_ITP(self, file_path: str): f.write(line + "\n") else: f.write("; " + line + "\n") - - f.write("\n[ moleculetype ]\n") - f.write(str(self.molecule_type) + "\n") + + if self.molecule_type is not None: + f.write("\n[ moleculetype ]\n") + f.write(str(self.molecule_type) + "\n") f.write("[ atoms ]\n") self.atoms = self._rearrange_atoms() @@ -363,18 +379,18 @@ def to_ITP(self, file_path: str): f.write(str(angle) + "\n") if any( - dihedral.dihedral_type.is_planar_constraint + dihedral.dihedral_type.is_planar_constraint or dihedral.dihedral_type.is_periodic_planar_constraint for dihedral in self.dihedrals ): f.write("\n[ dihedrals ]\n") - f.write("; GROMOS improper dihedrals\n") + f.write("; improper dihedrals\n") for dihedral in self.dihedrals: - if dihedral.dihedral_type.is_planar_constraint: + if dihedral.dihedral_type.is_planar_constraint or dihedral.dihedral_type.is_periodic_planar_constraint: f.write(str(dihedral) + "\n") f.write("\n[ dihedrals ]\n") for dihedral in self.dihedrals: - if dihedral.dihedral_type.is_rotational_constraint: + if dihedral.dihedral_type.is_rotational_constraint or dihedral.dihedral_type.is_rotational_constraint_with_constants: f.write(str(dihedral) + "\n") f.write("\n[ exclusions ]\n") @@ -899,7 +915,7 @@ def to_dict(self) -> dict: } @classmethod - def from_dict(cls, data: dict) -> Topology: + def from_dict(cls, data: dict, format: str = "gromos") -> Topology: """ Create a new Topology from a dictionary, such as that created with Topology.to_dict(). @@ -917,6 +933,9 @@ def from_dict(cls, data: dict) -> Topology: :param data: dictionary containing data to make a Topology, generate with 'to_dict()'. :type data: dict + :param format: The forcefield the ITP file is formatted as, options are + "gromos", "amber", "opls" and "charmm" + :type format: str, defaults to "gromos" for GROMOS forcefields. :return: a new Topology :rtype: Topology """ @@ -933,7 +952,7 @@ def from_dict(cls, data: dict) -> Topology: Angle.from_dict(angle_data,topology.atoms) for dihedral_data in data["dihedrals"]: - Dihedral.from_dict(dihedral_data,topology.atoms) + Dihedral.from_dict(dihedral_data,topology.atoms, format=format) for pair_data in data["pairs"]: Pair.from_dict(pair_data,topology.atoms) @@ -1049,7 +1068,7 @@ def change_atom(self, old_atom: Atom, new_atom: Atom): # change all the bonds for bond in old_atom.bonds: bond.clone_bond_changing(old_atom, new_atom) - + # change all the angles for bond in old_atom.bonds: for angle in bond.angles: diff --git a/tests/data/AMBER_PNIPAM_extend.itp b/tests/data/AMBER_PNIPAM_extend.itp new file mode 100644 index 0000000..3d3aec8 --- /dev/null +++ b/tests/data/AMBER_PNIPAM_extend.itp @@ -0,0 +1,323 @@ +[ atoms ] +; nr type resi res atom cgnr charge mass ; qtot bond_type + 1 c3 1 UNK C00 1 -0.092100 12.01000 ; qtot -0.092 + 2 c3 1 UNK C01 2 -0.079400 12.01000 ; qtot -0.171 + 3 c3 1 UNK C02 3 -0.072400 12.01000 ; qtot -0.244 + 4 c3 1 UNK C03 4 -0.127700 12.01000 ; qtot -0.372 + 5 c3 1 UNK C04 5 -0.072400 12.01000 ; qtot -0.444 + 6 c3 1 UNK C05 6 -0.099100 12.01000 ; qtot -0.543 + 7 c 1 UNK C06 7 0.661098 12.01000 ; qtot 0.118 + 8 o 1 UNK O07 8 -0.612100 16.00000 ; qtot -0.494 + 9 ns 1 UNK N08 9 -0.574900 14.01000 ; qtot -1.069 + 10 c3 1 UNK C09 10 0.095700 12.01000 ; qtot -0.973 + 11 c3 1 UNK C0A 11 -0.110100 12.01000 ; qtot -1.083 + 12 c3 1 UNK C0B 12 -0.110100 12.01000 ; qtot -1.194 + 13 hc 1 UNK H0C 13 0.034367 1.00800 ; qtot -1.159 + 14 hc 1 UNK H0D 14 0.034367 1.00800 ; qtot -1.125 + 15 hc 1 UNK H0E 15 0.034367 1.00800 ; qtot -1.090 + 16 hc 1 UNK H0F 16 0.036700 1.00800 ; qtot -1.054 + 17 hc 1 UNK H0G 17 0.036700 1.00800 ; qtot -1.017 + 18 hc 1 UNK H0H 18 0.059700 1.00800 ; qtot -0.957 + 19 hc 1 UNK H0I 19 0.059700 1.00800 ; qtot -0.898 + 20 hc 1 UNK H0J 20 0.056700 1.00800 ; qtot -0.841 + 21 hc 1 UNK H0K 21 0.040700 1.00800 ; qtot -0.800 + 22 hc 1 UNK H0M 22 0.040700 1.00800 ; qtot -0.760 + 23 hc 1 UNK H0N 23 0.042033 1.00800 ; qtot -0.717 + 24 hc 1 UNK H0O 24 0.042033 1.00800 ; qtot -0.675 + 25 hc 1 UNK H0P 25 0.042033 1.00800 ; qtot -0.633 + 26 hn 1 UNK H0Q 26 0.304500 1.00800 ; qtot -0.329 + 27 h1 1 UNK H0R 27 0.089700 1.00800 ; qtot -0.239 + 28 hc 1 UNK H0S 28 0.039867 1.00800 ; qtot -0.199 + 29 hc 1 UNK H0T 29 0.039867 1.00800 ; qtot -0.159 + 30 hc 1 UNK H0U 30 0.039867 1.00800 ; qtot -0.120 + 31 hc 1 UNK H0V 31 0.039867 1.00800 ; qtot -0.080 + 32 hc 1 UNK H0W 32 0.039867 1.00800 ; qtot -0.040 + 33 hc 1 UNK H0X 33 0.039867 1.00800 ; qtot 0.000 + +[ bonds ] +; ai aj funct r k + 1 2 1 1.5380e-01 1.9456e+05 ; C00 - C01 + 1 13 1 1.0970e-01 3.1455e+05 ; C00 - H0C + 1 14 1 1.0970e-01 3.1455e+05 ; C00 - H0D + 1 15 1 1.0970e-01 3.1455e+05 ; C00 - H0E + 2 3 1 1.5380e-01 1.9456e+05 ; C01 - C02 + 2 16 1 1.0970e-01 3.1455e+05 ; C01 - H0F + 2 17 1 1.0970e-01 3.1455e+05 ; C01 - H0G + 3 4 1 1.5380e-01 1.9456e+05 ; C02 - C03 + 3 18 1 1.0970e-01 3.1455e+05 ; C02 - H0H + 3 19 1 1.0970e-01 3.1455e+05 ; C02 - H0I + 4 5 1 1.5380e-01 1.9456e+05 ; C03 - C04 + 4 7 1 1.5240e-01 2.0351e+05 ; C03 - C06 + 4 20 1 1.0970e-01 3.1455e+05 ; C03 - H0J + 5 6 1 1.5380e-01 1.9456e+05 ; C04 - C05 + 5 21 1 1.0970e-01 3.1455e+05 ; C04 - H0K + 5 22 1 1.0970e-01 3.1455e+05 ; C04 - H0M + 6 23 1 1.0970e-01 3.1455e+05 ; C05 - H0N + 6 24 1 1.0970e-01 3.1455e+05 ; C05 - H0O + 6 25 1 1.0970e-01 3.1455e+05 ; C05 - H0P + 7 8 1 1.2180e-01 5.4610e+05 ; C06 - O07 + 7 9 1 1.3790e-01 2.9807e+05 ; C06 - N08 + 9 10 1 1.4620e-01 2.2075e+05 ; N08 - C09 + 9 26 1 1.0130e-01 4.4124e+05 ; N08 - H0Q + 10 11 1 1.5380e-01 1.9456e+05 ; C09 - C0A + 10 12 1 1.5380e-01 1.9456e+05 ; C09 - C0B + 10 27 1 1.0970e-01 3.1455e+05 ; C09 - H0R + 11 28 1 1.0970e-01 3.1455e+05 ; C0A - H0S + 11 29 1 1.0970e-01 3.1455e+05 ; C0A - H0T + 11 30 1 1.0970e-01 3.1455e+05 ; C0A - H0U + 12 31 1 1.0970e-01 3.1455e+05 ; C0B - H0V + 12 32 1 1.0970e-01 3.1455e+05 ; C0B - H0W + 12 33 1 1.0970e-01 3.1455e+05 ; C0B - H0X + +[ pairs ] +; ai aj funct + 1 4 1 ; C00 - C03 + 1 18 1 ; C00 - H0H + 1 19 1 ; C00 - H0I + 2 5 1 ; C01 - C04 + 2 7 1 ; C01 - C06 + 2 20 1 ; C01 - H0J + 3 6 1 ; C02 - C05 + 3 8 1 ; C02 - O07 + 3 9 1 ; C02 - N08 + 3 21 1 ; C02 - H0K + 3 22 1 ; C02 - H0M + 4 10 1 ; C03 - C09 + 4 16 1 ; C03 - H0F + 4 17 1 ; C03 - H0G + 4 23 1 ; C03 - H0N + 4 24 1 ; C03 - H0O + 4 25 1 ; C03 - H0P + 4 26 1 ; C03 - H0Q + 5 8 1 ; C04 - O07 + 5 9 1 ; C04 - N08 + 5 18 1 ; C04 - H0H + 5 19 1 ; C04 - H0I + 6 7 1 ; C05 - C06 + 6 20 1 ; C05 - H0J + 7 11 1 ; C06 - C0A + 7 12 1 ; C06 - C0B + 7 18 1 ; C06 - H0H + 7 19 1 ; C06 - H0I + 7 21 1 ; C06 - H0K + 7 22 1 ; C06 - H0M + 7 27 1 ; C06 - H0R + 8 10 1 ; O07 - C09 + 8 20 1 ; O07 - H0J + 8 26 1 ; O07 - H0Q + 9 20 1 ; N08 - H0J + 9 28 1 ; N08 - H0S + 9 29 1 ; N08 - H0T + 9 30 1 ; N08 - H0U + 9 31 1 ; N08 - H0V + 9 32 1 ; N08 - H0W + 9 33 1 ; N08 - H0X + 11 26 1 ; C0A - H0Q + 11 31 1 ; C0A - H0V + 11 32 1 ; C0A - H0W + 11 33 1 ; C0A - H0X + 12 26 1 ; C0B - H0Q + 12 28 1 ; C0B - H0S + 12 29 1 ; C0B - H0T + 12 30 1 ; C0B - H0U + 13 3 1 ; H0C - C02 + 13 16 1 ; H0C - H0F + 13 17 1 ; H0C - H0G + 14 3 1 ; H0D - C02 + 14 16 1 ; H0D - H0F + 14 17 1 ; H0D - H0G + 15 3 1 ; H0E - C02 + 15 16 1 ; H0E - H0F + 15 17 1 ; H0E - H0G + 16 18 1 ; H0F - H0H + 16 19 1 ; H0F - H0I + 17 18 1 ; H0G - H0H + 17 19 1 ; H0G - H0I + 18 20 1 ; H0H - H0J + 19 20 1 ; H0I - H0J + 20 21 1 ; H0J - H0K + 20 22 1 ; H0J - H0M + 21 23 1 ; H0K - H0N + 21 24 1 ; H0K - H0O + 21 25 1 ; H0K - H0P + 22 23 1 ; H0M - H0N + 22 24 1 ; H0M - H0O + 22 25 1 ; H0M - H0P + 26 27 1 ; H0Q - H0R + 27 28 1 ; H0R - H0S + 27 29 1 ; H0R - H0T + 27 30 1 ; H0R - H0U + 27 31 1 ; H0R - H0V + 27 32 1 ; H0R - H0W + 27 33 1 ; H0R - H0X + +[ angles ] +; ai aj ak funct theta cth + 1 2 3 1 1.1151e+02 5.4308e+02 ; C00 - C01 - C02 + 1 2 16 1 1.0980e+02 3.9162e+02 ; C00 - C01 - H0F + 1 2 17 1 1.0980e+02 3.9162e+02 ; C00 - C01 - H0G + 2 1 13 1 1.0980e+02 3.9162e+02 ; C01 - C00 - H0C + 2 1 14 1 1.0980e+02 3.9162e+02 ; C01 - C00 - H0D + 2 1 15 1 1.0980e+02 3.9162e+02 ; C01 - C00 - H0E + 2 3 4 1 1.1151e+02 5.4308e+02 ; C01 - C02 - C03 + 2 3 18 1 1.0980e+02 3.9162e+02 ; C01 - C02 - H0H + 2 3 19 1 1.0980e+02 3.9162e+02 ; C01 - C02 - H0I + 3 2 16 1 1.0980e+02 3.9162e+02 ; C02 - C01 - H0F + 3 2 17 1 1.0980e+02 3.9162e+02 ; C02 - C01 - H0G + 3 4 5 1 1.1151e+02 5.4308e+02 ; C02 - C03 - C04 + 3 4 7 1 1.1104e+02 5.4643e+02 ; C02 - C03 - C06 + 3 4 20 1 1.0980e+02 3.9162e+02 ; C02 - C03 - H0J + 4 3 18 1 1.0980e+02 3.9162e+02 ; C03 - C02 - H0H + 4 3 19 1 1.0980e+02 3.9162e+02 ; C03 - C02 - H0I + 4 5 6 1 1.1151e+02 5.4308e+02 ; C03 - C04 - C05 + 4 5 21 1 1.0980e+02 3.9162e+02 ; C03 - C04 - H0K + 4 5 22 1 1.0980e+02 3.9162e+02 ; C03 - C04 - H0M + 4 7 8 1 1.2320e+02 7.0793e+02 ; C03 - C06 - O07 + 4 7 9 1 1.1518e+02 7.0542e+02 ; C03 - C06 - N08 + 5 4 7 1 1.1104e+02 5.4643e+02 ; C04 - C03 - C06 + 5 4 20 1 1.0980e+02 3.9162e+02 ; C04 - C03 - H0J + 5 6 23 1 1.0980e+02 3.9162e+02 ; C04 - C05 - H0N + 5 6 24 1 1.0980e+02 3.9162e+02 ; C04 - C05 - H0O + 5 6 25 1 1.0980e+02 3.9162e+02 ; C04 - C05 - H0P + 6 5 21 1 1.0980e+02 3.9162e+02 ; C05 - C04 - H0K + 6 5 22 1 1.0980e+02 3.9162e+02 ; C05 - C04 - H0M + 7 4 20 1 1.0877e+02 3.9664e+02 ; C06 - C03 - H0J + 7 9 10 1 1.2069e+02 5.4643e+02 ; C06 - N08 - C09 + 7 9 26 1 1.1755e+02 4.0752e+02 ; C06 - N08 - H0Q + 8 7 9 1 1.2305e+02 9.5228e+02 ; O07 - C06 - N08 + 9 10 11 1 1.1161e+02 6.9622e+02 ; N08 - C09 - C0A + 9 10 12 1 1.1161e+02 6.9622e+02 ; N08 - C09 - C0B + 9 10 27 1 1.0888e+02 5.1463e+02 ; N08 - C09 - H0R + 10 9 26 1 1.1768e+02 3.8576e+02 ; C09 - N08 - H0Q + 10 11 28 1 1.0980e+02 3.9162e+02 ; C09 - C0A - H0S + 10 11 29 1 1.0980e+02 3.9162e+02 ; C09 - C0A - H0T + 10 11 30 1 1.0980e+02 3.9162e+02 ; C09 - C0A - H0U + 10 12 31 1 1.0980e+02 3.9162e+02 ; C09 - C0B - H0V + 10 12 32 1 1.0980e+02 3.9162e+02 ; C09 - C0B - H0W + 10 12 33 1 1.0980e+02 3.9162e+02 ; C09 - C0B - H0X + 11 10 12 1 1.1151e+02 5.4308e+02 ; C0A - C09 - C0B + 11 10 27 1 1.0956e+02 3.9246e+02 ; C0A - C09 - H0R + 12 10 27 1 1.0956e+02 3.9246e+02 ; C0B - C09 - H0R + 13 1 14 1 1.0758e+02 3.2635e+02 ; H0C - C00 - H0D + 13 1 15 1 1.0758e+02 3.2635e+02 ; H0C - C00 - H0E + 14 1 15 1 1.0758e+02 3.2635e+02 ; H0D - C00 - H0E + 16 2 17 1 1.0758e+02 3.2635e+02 ; H0F - C01 - H0G + 18 3 19 1 1.0758e+02 3.2635e+02 ; H0H - C02 - H0I + 21 5 22 1 1.0758e+02 3.2635e+02 ; H0K - C04 - H0M + 23 6 24 1 1.0758e+02 3.2635e+02 ; H0N - C05 - H0O + 23 6 25 1 1.0758e+02 3.2635e+02 ; H0N - C05 - H0P + 24 6 25 1 1.0758e+02 3.2635e+02 ; H0O - C05 - H0P + 28 11 29 1 1.0758e+02 3.2635e+02 ; H0S - C0A - H0T + 28 11 30 1 1.0758e+02 3.2635e+02 ; H0S - C0A - H0U + 29 11 30 1 1.0758e+02 3.2635e+02 ; H0T - C0A - H0U + 31 12 32 1 1.0758e+02 3.2635e+02 ; H0V - C0B - H0W + 31 12 33 1 1.0758e+02 3.2635e+02 ; H0V - C0B - H0X + 32 12 33 1 1.0758e+02 3.2635e+02 ; H0W - C0B - H0X + +[ dihedrals ] ; propers +; for gromacs 4.5 or higher, using funct 9 +; i j k l func phase kd pn + 1 2 3 4 9 0.00 0.46024 1 ; C00- C01- C02- C03 + 1 2 3 4 9 0.00 0.54392 3 ; C00- C01- C02- C03 + 1 2 3 4 9 180.00 1.21336 2 ; C00- C01- C02- C03 + 1 2 3 18 9 0.00 0.33472 3 ; C00- C01- C02- H0H + 1 2 3 19 9 0.00 0.33472 3 ; C00- C01- C02- H0I + 2 3 4 5 9 0.00 0.46024 1 ; C01- C02- C03- C04 + 2 3 4 5 9 0.00 0.54392 3 ; C01- C02- C03- C04 + 2 3 4 5 9 180.00 1.21336 2 ; C01- C02- C03- C04 + 2 3 4 7 9 0.00 0.41840 3 ; C01- C02- C03- C06 + 2 3 4 20 9 0.00 0.33472 3 ; C01- C02- C03- H0J + 3 4 5 6 9 0.00 0.46024 1 ; C02- C03- C04- C05 + 3 4 5 6 9 0.00 0.54392 3 ; C02- C03- C04- C05 + 3 4 5 6 9 180.00 1.21336 2 ; C02- C03- C04- C05 + 3 4 5 21 9 0.00 0.33472 3 ; C02- C03- C04- H0K + 3 4 5 22 9 0.00 0.33472 3 ; C02- C03- C04- H0M + 3 4 7 8 9 0.00 3.09616 1 ; C02- C03- C06- O07 + 3 4 7 8 9 180.00 1.12968 2 ; C02- C03- C06- O07 + 3 4 7 8 9 180.00 2.30120 3 ; C02- C03- C06- O07 + 3 4 7 9 9 180.00 0.00000 4 ; C02- C03- C06- N08 + 3 4 7 9 9 180.00 2.97064 2 ; C02- C03- C06- N08 + 4 3 2 16 9 0.00 0.33472 3 ; C03- C02- C01- H0F + 4 3 2 17 9 0.00 0.33472 3 ; C03- C02- C01- H0G + 4 5 6 23 9 0.00 0.33472 3 ; C03- C04- C05- H0N + 4 5 6 24 9 0.00 0.33472 3 ; C03- C04- C05- H0O + 4 5 6 25 9 0.00 0.33472 3 ; C03- C04- C05- H0P + 4 7 9 10 9 0.00 2.09200 1 ; C03- C06- N08- C09 + 4 7 9 10 9 180.00 1.08784 2 ; C03- C06- N08- C09 + 4 7 9 26 9 180.00 10.46000 2 ; C03- C06- N08- H0Q + 5 4 3 18 9 0.00 0.33472 3 ; C04- C03- C02- H0H + 5 4 3 19 9 0.00 0.33472 3 ; C04- C03- C02- H0I + 5 4 7 8 9 0.00 3.09616 1 ; C04- C03- C06- O07 + 5 4 7 8 9 180.00 1.12968 2 ; C04- C03- C06- O07 + 5 4 7 8 9 180.00 2.30120 3 ; C04- C03- C06- O07 + 5 4 7 9 9 180.00 0.00000 4 ; C04- C03- C06- N08 + 5 4 7 9 9 180.00 2.97064 2 ; C04- C03- C06- N08 + 6 5 4 7 9 0.00 0.41840 3 ; C05- C04- C03- C06 + 6 5 4 20 9 0.00 0.33472 3 ; C05- C04- C03- H0J + 7 4 3 18 9 0.00 0.65084 3 ; C06- C03- C02- H0H + 7 4 3 19 9 0.00 0.65084 3 ; C06- C03- C02- H0I + 7 4 5 21 9 0.00 0.65084 3 ; C06- C03- C04- H0K + 7 4 5 22 9 0.00 0.65084 3 ; C06- C03- C04- H0M + 7 9 10 11 9 0.00 0.71128 3 ; C06- N08- C09- C0A + 7 9 10 11 9 180.00 0.41840 4 ; C06- N08- C09- C0A + 7 9 10 11 9 180.00 4.26768 1 ; C06- N08- C09- C0A + 7 9 10 12 9 0.00 0.71128 3 ; C06- N08- C09- C0B + 7 9 10 12 9 180.00 0.41840 4 ; C06- N08- C09- C0B + 7 9 10 12 9 180.00 4.26768 1 ; C06- N08- C09- C0B + 7 9 10 27 9 180.00 0.00000 2 ; C06- N08- C09- H0R + 8 7 4 20 9 0.00 3.47272 1 ; O07- C06- C03- H0J + 8 7 4 20 9 180.00 0.16736 3 ; O07- C06- C03- H0J + 8 7 9 10 9 180.00 10.46000 2 ; O07- C06- N08- C09 + 8 7 9 26 9 0.00 8.36800 1 ; O07- C06- N08- H0Q + 8 7 9 26 9 180.00 10.46000 2 ; O07- C06- N08- H0Q + 9 7 4 20 9 180.00 0.00000 2 ; N08- C06- C03- H0J + 9 10 11 28 9 0.00 0.65084 3 ; N08- C09- C0A- H0S + 9 10 11 29 9 0.00 0.65084 3 ; N08- C09- C0A- H0T + 9 10 11 30 9 0.00 0.65084 3 ; N08- C09- C0A- H0U + 9 10 12 31 9 0.00 0.65084 3 ; N08- C09- C0B- H0V + 9 10 12 32 9 0.00 0.65084 3 ; N08- C09- C0B- H0W + 9 10 12 33 9 0.00 0.65084 3 ; N08- C09- C0B- H0X + 11 10 9 26 9 0.00 0.00000 0 ; C0A- C09- N08- H0Q + 11 10 12 31 9 0.00 0.33472 3 ; C0A- C09- C0B- H0V + 11 10 12 32 9 0.00 0.33472 3 ; C0A- C09- C0B- H0W + 11 10 12 33 9 0.00 0.33472 3 ; C0A- C09- C0B- H0X + 12 10 9 26 9 0.00 0.00000 0 ; C0B- C09- N08- H0Q + 12 10 11 28 9 0.00 0.33472 3 ; C0B- C09- C0A- H0S + 12 10 11 29 9 0.00 0.33472 3 ; C0B- C09- C0A- H0T + 12 10 11 30 9 0.00 0.33472 3 ; C0B- C09- C0A- H0U + 13 1 2 3 9 0.00 0.33472 3 ; H0C- C00- C01- C02 + 13 1 2 16 9 0.00 0.50208 3 ; H0C- C00- C01- H0F + 13 1 2 17 9 0.00 0.50208 3 ; H0C- C00- C01- H0G + 14 1 2 3 9 0.00 0.33472 3 ; H0D- C00- C01- C02 + 14 1 2 16 9 0.00 0.50208 3 ; H0D- C00- C01- H0F + 14 1 2 17 9 0.00 0.50208 3 ; H0D- C00- C01- H0G + 15 1 2 3 9 0.00 0.33472 3 ; H0E- C00- C01- C02 + 15 1 2 16 9 0.00 0.50208 3 ; H0E- C00- C01- H0F + 15 1 2 17 9 0.00 0.50208 3 ; H0E- C00- C01- H0G + 16 2 3 18 9 0.00 0.50208 3 ; H0F- C01- C02- H0H + 16 2 3 19 9 0.00 0.50208 3 ; H0F- C01- C02- H0I + 17 2 3 18 9 0.00 0.50208 3 ; H0G- C01- C02- H0H + 17 2 3 19 9 0.00 0.50208 3 ; H0G- C01- C02- H0I + 18 3 4 20 9 0.00 0.50208 3 ; H0H- C02- C03- H0J + 19 3 4 20 9 0.00 0.50208 3 ; H0I- C02- C03- H0J + 20 4 5 21 9 0.00 0.50208 3 ; H0J- C03- C04- H0K + 20 4 5 22 9 0.00 0.50208 3 ; H0J- C03- C04- H0M + 21 5 6 23 9 0.00 0.50208 3 ; H0K- C04- C05- H0N + 21 5 6 24 9 0.00 0.50208 3 ; H0K- C04- C05- H0O + 21 5 6 25 9 0.00 0.50208 3 ; H0K- C04- C05- H0P + 22 5 6 23 9 0.00 0.50208 3 ; H0M- C04- C05- H0N + 22 5 6 24 9 0.00 0.50208 3 ; H0M- C04- C05- H0O + 22 5 6 25 9 0.00 0.50208 3 ; H0M- C04- C05- H0P + 26 9 10 27 9 0.00 0.00000 0 ; H0Q- N08- C09- H0R + 27 10 11 28 9 0.00 0.65084 3 ; H0R- C09- C0A- H0S + 27 10 11 29 9 0.00 0.65084 3 ; H0R- C09- C0A- H0T + 27 10 11 30 9 0.00 0.65084 3 ; H0R- C09- C0A- H0U + 27 10 12 31 9 0.00 0.65084 3 ; H0R- C09- C0B- H0V + 27 10 12 32 9 0.00 0.65084 3 ; H0R- C09- C0B- H0W + 27 10 12 33 9 0.00 0.65084 3 ; H0R- C09- C0B- H0X + +[ dihedrals ] ; impropers +; treated as propers in GROMACS to use correct AMBER analytical function +; i j k l func phase kd pn + 4 9 7 8 4 180.00 43.93200 2 ; C03- N08- C06- O07 + 7 10 9 26 4 180.00 4.60240 2 ; C06- C09- N08- H0Q diff --git a/tests/data/AMBER_pnipam_GMX.itp b/tests/data/AMBER_pnipam_GMX.itp new file mode 100644 index 0000000..35dda60 --- /dev/null +++ b/tests/data/AMBER_pnipam_GMX.itp @@ -0,0 +1,259 @@ +[ atoms ] +; nr type resi res atom cgnr charge mass ; qtot bond_type + 1 o 1 UNL O 1 -0.612100 16.00000 ; qtot -0.612 + 2 ns 1 UNL N 2 -0.575900 14.01000 ; qtot -1.188 + 3 c3 1 UNL C 3 -0.131700 12.01000 ; qtot -1.320 + 4 c3 1 UNL C1 4 -0.072400 12.01000 ; qtot -1.392 + 5 c3 1 UNL C2 5 0.096700 12.01000 ; qtot -1.295 + 6 c 1 UNL C3 6 0.664102 12.01000 ; qtot -0.631 + 7 c3 1 UNL C4 7 -0.092100 12.01000 ; qtot -0.723 + 8 c3 1 UNL C5 8 -0.096100 12.01000 ; qtot -0.819 + 9 c3 1 UNL C6 9 -0.110100 12.01000 ; qtot -0.930 + 10 c3 1 UNL C7 10 -0.110100 12.01000 ; qtot -1.040 + 11 hc 1 UNL H 11 0.057700 1.00800 ; qtot -0.982 + 12 hc 1 UNL H1 12 0.054700 1.00800 ; qtot -0.927 + 13 hc 1 UNL H2 13 0.054700 1.00800 ; qtot -0.873 + 14 h1 1 UNL H3 14 0.089700 1.00800 ; qtot -0.783 + 15 hn 1 UNL H4 15 0.304500 1.00800 ; qtot -0.478 + 16 hc 1 UNL H5 16 0.043033 1.00800 ; qtot -0.435 + 17 hc 1 UNL H6 17 0.043033 1.00800 ; qtot -0.392 + 18 hc 1 UNL H7 18 0.043033 1.00800 ; qtot -0.349 + 19 hc 1 UNL H8 19 0.037033 1.00800 ; qtot -0.312 + 20 hc 1 UNL H9 20 0.037033 1.00800 ; qtot -0.275 + 21 hc 1 UNL H10 21 0.037033 1.00800 ; qtot -0.238 + 22 hc 1 UNL H11 22 0.039700 1.00800 ; qtot -0.199 + 23 hc 1 UNL H12 23 0.039700 1.00800 ; qtot -0.159 + 24 hc 1 UNL H13 24 0.039700 1.00800 ; qtot -0.119 + 25 hc 1 UNL H14 25 0.039700 1.00800 ; qtot -0.079 + 26 hc 1 UNL H15 26 0.039700 1.00800 ; qtot -0.040 + 27 hc 1 UNL H16 27 0.039700 1.00800 ; qtot -0.000 + +[ bonds ] +; ai aj funct r k + 1 6 1 1.2180e-01 5.4610e+05 ; O - C3 + 2 5 1 1.4620e-01 2.2075e+05 ; N - C2 + 2 6 1 1.3790e-01 2.9807e+05 ; N - C3 + 2 15 1 1.0130e-01 4.4124e+05 ; N - H4 + 3 4 1 1.5380e-01 1.9456e+05 ; C - C1 + 3 6 1 1.5240e-01 2.0351e+05 ; C - C3 + 3 7 1 1.5380e-01 1.9456e+05 ; C - C4 + 3 11 1 1.0970e-01 3.1455e+05 ; C - H + 4 8 1 1.5380e-01 1.9456e+05 ; C1 - C5 + 4 12 1 1.0970e-01 3.1455e+05 ; C1 - H1 + 4 13 1 1.0970e-01 3.1455e+05 ; C1 - H2 + 5 9 1 1.5380e-01 1.9456e+05 ; C2 - C6 + 5 10 1 1.5380e-01 1.9456e+05 ; C2 - C7 + 5 14 1 1.0970e-01 3.1455e+05 ; C2 - H3 + 7 16 1 1.0970e-01 3.1455e+05 ; C4 - H5 + 7 17 1 1.0970e-01 3.1455e+05 ; C4 - H6 + 7 18 1 1.0970e-01 3.1455e+05 ; C4 - H7 + 8 19 1 1.0970e-01 3.1455e+05 ; C5 - H8 + 8 20 1 1.0970e-01 3.1455e+05 ; C5 - H9 + 8 21 1 1.0970e-01 3.1455e+05 ; C5 - H10 + 9 22 1 1.0970e-01 3.1455e+05 ; C6 - H11 + 9 23 1 1.0970e-01 3.1455e+05 ; C6 - H12 + 9 24 1 1.0970e-01 3.1455e+05 ; C6 - H13 + 10 25 1 1.0970e-01 3.1455e+05 ; C7 - H14 + 10 26 1 1.0970e-01 3.1455e+05 ; C7 - H15 + 10 27 1 1.0970e-01 3.1455e+05 ; C7 - H16 + +[ pairs ] +; ai aj funct + 1 4 1 ; O - C1 + 1 5 1 ; O - C2 + 1 7 1 ; O - C4 + 1 11 1 ; O - H + 1 15 1 ; O - H4 + 2 4 1 ; N - C1 + 2 7 1 ; N - C4 + 2 11 1 ; N - H + 2 22 1 ; N - H11 + 2 23 1 ; N - H12 + 2 24 1 ; N - H13 + 2 25 1 ; N - H14 + 2 26 1 ; N - H15 + 2 27 1 ; N - H16 + 3 5 1 ; C - C2 + 3 15 1 ; C - H4 + 3 19 1 ; C - H8 + 3 20 1 ; C - H9 + 3 21 1 ; C - H10 + 4 16 1 ; C1 - H5 + 4 17 1 ; C1 - H6 + 4 18 1 ; C1 - H7 + 6 8 1 ; C3 - C5 + 6 9 1 ; C3 - C6 + 6 10 1 ; C3 - C7 + 6 12 1 ; C3 - H1 + 6 13 1 ; C3 - H2 + 6 14 1 ; C3 - H3 + 6 16 1 ; C3 - H5 + 6 17 1 ; C3 - H6 + 6 18 1 ; C3 - H7 + 7 8 1 ; C4 - C5 + 7 12 1 ; C4 - H1 + 7 13 1 ; C4 - H2 + 8 11 1 ; C5 - H + 9 15 1 ; C6 - H4 + 9 25 1 ; C6 - H14 + 9 26 1 ; C6 - H15 + 9 27 1 ; C6 - H16 + 10 15 1 ; C7 - H4 + 10 22 1 ; C7 - H11 + 10 23 1 ; C7 - H12 + 10 24 1 ; C7 - H13 + 11 12 1 ; H - H1 + 11 13 1 ; H - H2 + 11 16 1 ; H - H5 + 11 17 1 ; H - H6 + 11 18 1 ; H - H7 + 12 19 1 ; H1 - H8 + 12 20 1 ; H1 - H9 + 12 21 1 ; H1 - H10 + 13 19 1 ; H2 - H8 + 13 20 1 ; H2 - H9 + 13 21 1 ; H2 - H10 + 14 15 1 ; H3 - H4 + 14 22 1 ; H3 - H11 + 14 23 1 ; H3 - H12 + 14 24 1 ; H3 - H13 + 14 25 1 ; H3 - H14 + 14 26 1 ; H3 - H15 + 14 27 1 ; H3 - H16 + +[ angles ] +; ai aj ak funct theta cth + 1 6 2 1 1.2305e+02 9.5228e+02 ; O - C3 - N + 1 6 3 1 1.2320e+02 7.0793e+02 ; O - C3 - C + 2 5 9 1 1.1161e+02 6.9622e+02 ; N - C2 - C6 + 2 5 10 1 1.1161e+02 6.9622e+02 ; N - C2 - C7 + 2 5 14 1 1.0888e+02 5.1463e+02 ; N - C2 - H3 + 2 6 3 1 1.1518e+02 7.0542e+02 ; N - C3 - C + 3 4 8 1 1.1151e+02 5.4308e+02 ; C - C1 - C5 + 3 4 12 1 1.0980e+02 3.9162e+02 ; C - C1 - H1 + 3 4 13 1 1.0980e+02 3.9162e+02 ; C - C1 - H2 + 3 7 16 1 1.0980e+02 3.9162e+02 ; C - C4 - H5 + 3 7 17 1 1.0980e+02 3.9162e+02 ; C - C4 - H6 + 3 7 18 1 1.0980e+02 3.9162e+02 ; C - C4 - H7 + 4 3 6 1 1.1104e+02 5.4643e+02 ; C1 - C - C3 + 4 3 7 1 1.1151e+02 5.4308e+02 ; C1 - C - C4 + 4 3 11 1 1.0980e+02 3.9162e+02 ; C1 - C - H + 4 8 19 1 1.0980e+02 3.9162e+02 ; C1 - C5 - H8 + 4 8 20 1 1.0980e+02 3.9162e+02 ; C1 - C5 - H9 + 4 8 21 1 1.0980e+02 3.9162e+02 ; C1 - C5 - H10 + 5 2 6 1 1.2069e+02 5.4643e+02 ; C2 - N - C3 + 5 2 15 1 1.1768e+02 3.8576e+02 ; C2 - N - H4 + 5 9 22 1 1.0980e+02 3.9162e+02 ; C2 - C6 - H11 + 5 9 23 1 1.0980e+02 3.9162e+02 ; C2 - C6 - H12 + 5 9 24 1 1.0980e+02 3.9162e+02 ; C2 - C6 - H13 + 5 10 25 1 1.0980e+02 3.9162e+02 ; C2 - C7 - H14 + 5 10 26 1 1.0980e+02 3.9162e+02 ; C2 - C7 - H15 + 5 10 27 1 1.0980e+02 3.9162e+02 ; C2 - C7 - H16 + 6 2 15 1 1.1755e+02 4.0752e+02 ; C3 - N - H4 + 6 3 7 1 1.1104e+02 5.4643e+02 ; C3 - C - C4 + 6 3 11 1 1.0877e+02 3.9664e+02 ; C3 - C - H + 7 3 11 1 1.0980e+02 3.9162e+02 ; C4 - C - H + 8 4 12 1 1.0980e+02 3.9162e+02 ; C5 - C1 - H1 + 8 4 13 1 1.0980e+02 3.9162e+02 ; C5 - C1 - H2 + 9 5 10 1 1.1151e+02 5.4308e+02 ; C6 - C2 - C7 + 9 5 14 1 1.0956e+02 3.9246e+02 ; C6 - C2 - H3 + 10 5 14 1 1.0956e+02 3.9246e+02 ; C7 - C2 - H3 + 12 4 13 1 1.0758e+02 3.2635e+02 ; H1 - C1 - H2 + 16 7 17 1 1.0758e+02 3.2635e+02 ; H5 - C4 - H6 + 16 7 18 1 1.0758e+02 3.2635e+02 ; H5 - C4 - H7 + 17 7 18 1 1.0758e+02 3.2635e+02 ; H6 - C4 - H7 + 19 8 20 1 1.0758e+02 3.2635e+02 ; H8 - C5 - H9 + 19 8 21 1 1.0758e+02 3.2635e+02 ; H8 - C5 - H10 + 20 8 21 1 1.0758e+02 3.2635e+02 ; H9 - C5 - H10 + 22 9 23 1 1.0758e+02 3.2635e+02 ; H11 - C6 - H12 + 22 9 24 1 1.0758e+02 3.2635e+02 ; H11 - C6 - H13 + 23 9 24 1 1.0758e+02 3.2635e+02 ; H12 - C6 - H13 + 25 10 26 1 1.0758e+02 3.2635e+02 ; H14 - C7 - H15 + 25 10 27 1 1.0758e+02 3.2635e+02 ; H14 - C7 - H16 + 26 10 27 1 1.0758e+02 3.2635e+02 ; H15 - C7 - H16 + +[ dihedrals ] ; propers +; for gromacs 4.5 or higher, using funct 9 +; i j k l func phase kd pn + 1 6 2 5 9 180.00 10.46000 2 ; O- C3- N- C2 + 1 6 2 15 9 0.00 8.36800 1 ; O- C3- N- H4 + 1 6 2 15 9 180.00 10.46000 2 ; O- C3- N- H4 + 1 6 3 4 9 0.00 3.09616 1 ; O- C3- C- C1 + 1 6 3 4 9 180.00 1.12968 2 ; O- C3- C- C1 + 1 6 3 4 9 180.00 2.30120 3 ; O- C3- C- C1 + 1 6 3 7 9 0.00 3.09616 1 ; O- C3- C- C4 + 1 6 3 7 9 180.00 1.12968 2 ; O- C3- C- C4 + 1 6 3 7 9 180.00 2.30120 3 ; O- C3- C- C4 + 1 6 3 11 9 0.00 3.47272 1 ; O- C3- C- H + 1 6 3 11 9 180.00 0.16736 3 ; O- C3- C- H + 2 5 9 22 9 0.00 0.65084 3 ; N- C2- C6- H11 + 2 5 9 23 9 0.00 0.65084 3 ; N- C2- C6- H12 + 2 5 9 24 9 0.00 0.65084 3 ; N- C2- C6- H13 + 2 5 10 25 9 0.00 0.65084 3 ; N- C2- C7- H14 + 2 5 10 26 9 0.00 0.65084 3 ; N- C2- C7- H15 + 2 5 10 27 9 0.00 0.65084 3 ; N- C2- C7- H16 + 2 6 3 4 9 180.00 0.00000 4 ; N- C3- C- C1 + 2 6 3 4 9 180.00 2.97064 2 ; N- C3- C- C1 + 2 6 3 7 9 180.00 0.00000 4 ; N- C3- C- C4 + 2 6 3 7 9 180.00 2.97064 2 ; N- C3- C- C4 + 2 6 3 11 9 180.00 0.00000 2 ; N- C3- C- H + 3 4 8 19 9 0.00 0.33472 3 ; C- C1- C5- H8 + 3 4 8 20 9 0.00 0.33472 3 ; C- C1- C5- H9 + 3 4 8 21 9 0.00 0.33472 3 ; C- C1- C5- H10 + 3 6 2 5 9 0.00 2.09200 1 ; C- C3- N- C2 + 3 6 2 5 9 180.00 1.08784 2 ; C- C3- N- C2 + 3 6 2 15 9 180.00 10.46000 2 ; C- C3- N- H4 + 4 3 7 16 9 0.00 0.33472 3 ; C1- C- C4- H5 + 4 3 7 17 9 0.00 0.33472 3 ; C1- C- C4- H6 + 4 3 7 18 9 0.00 0.33472 3 ; C1- C- C4- H7 + 6 2 5 9 9 0.00 0.71128 3 ; C3- N- C2- C6 + 6 2 5 9 9 180.00 0.41840 4 ; C3- N- C2- C6 + 6 2 5 9 9 180.00 4.26768 1 ; C3- N- C2- C6 + 6 2 5 10 9 0.00 0.71128 3 ; C3- N- C2- C7 + 6 2 5 10 9 180.00 0.41840 4 ; C3- N- C2- C7 + 6 2 5 10 9 180.00 4.26768 1 ; C3- N- C2- C7 + 6 2 5 14 9 180.00 0.00000 2 ; C3- N- C2- H3 + 6 3 4 8 9 0.00 0.41840 3 ; C3- C- C1- C5 + 6 3 4 12 9 0.00 0.65084 3 ; C3- C- C1- H1 + 6 3 4 13 9 0.00 0.65084 3 ; C3- C- C1- H2 + 6 3 7 16 9 0.00 0.65084 3 ; C3- C- C4- H5 + 6 3 7 17 9 0.00 0.65084 3 ; C3- C- C4- H6 + 6 3 7 18 9 0.00 0.65084 3 ; C3- C- C4- H7 + 7 3 4 8 9 0.00 0.46024 1 ; C4- C- C1- C5 + 7 3 4 8 9 0.00 0.54392 3 ; C4- C- C1- C5 + 7 3 4 8 9 180.00 1.21336 2 ; C4- C- C1- C5 + 7 3 4 12 9 0.00 0.33472 3 ; C4- C- C1- H1 + 7 3 4 13 9 0.00 0.33472 3 ; C4- C- C1- H2 + 8 4 3 11 9 0.00 0.33472 3 ; C5- C1- C- H + 9 5 2 15 9 0.00 0.00000 0 ; C6- C2- N- H4 + 9 5 10 25 9 0.00 0.33472 3 ; C6- C2- C7- H14 + 9 5 10 26 9 0.00 0.33472 3 ; C6- C2- C7- H15 + 9 5 10 27 9 0.00 0.33472 3 ; C6- C2- C7- H16 + 10 5 2 15 9 0.00 0.00000 0 ; C7- C2- N- H4 + 10 5 9 22 9 0.00 0.33472 3 ; C7- C2- C6- H11 + 10 5 9 23 9 0.00 0.33472 3 ; C7- C2- C6- H12 + 10 5 9 24 9 0.00 0.33472 3 ; C7- C2- C6- H13 + 11 3 4 12 9 0.00 0.50208 3 ; H- C- C1- H1 + 11 3 4 13 9 0.00 0.50208 3 ; H- C- C1- H2 + 11 3 7 16 9 0.00 0.50208 3 ; H- C- C4- H5 + 11 3 7 17 9 0.00 0.50208 3 ; H- C- C4- H6 + 11 3 7 18 9 0.00 0.50208 3 ; H- C- C4- H7 + 12 4 8 19 9 0.00 0.50208 3 ; H1- C1- C5- H8 + 12 4 8 20 9 0.00 0.50208 3 ; H1- C1- C5- H9 + 12 4 8 21 9 0.00 0.50208 3 ; H1- C1- C5- H10 + 13 4 8 19 9 0.00 0.50208 3 ; H2- C1- C5- H8 + 13 4 8 20 9 0.00 0.50208 3 ; H2- C1- C5- H9 + 13 4 8 21 9 0.00 0.50208 3 ; H2- C1- C5- H10 + 14 5 2 15 9 0.00 0.00000 0 ; H3- C2- N- H4 + 14 5 9 22 9 0.00 0.65084 3 ; H3- C2- C6- H11 + 14 5 9 23 9 0.00 0.65084 3 ; H3- C2- C6- H12 + 14 5 9 24 9 0.00 0.65084 3 ; H3- C2- C6- H13 + 14 5 10 25 9 0.00 0.65084 3 ; H3- C2- C7- H14 + 14 5 10 26 9 0.00 0.65084 3 ; H3- C2- C7- H15 + 14 5 10 27 9 0.00 0.65084 3 ; H3- C2- C7- H16 + +[ dihedrals ] ; impropers +; treated as propers in GROMACS to use correct AMBER analytical function +; i j k l func phase kd pn + 1 6 2 3 4 180.00 43.93200 2 ; O- C3- N- C + 6 5 2 15 4 180.00 4.60240 2 ; C3- C2- N- H4 diff --git a/tests/data/CHARMM_PNIPAM_extend.itp b/tests/data/CHARMM_PNIPAM_extend.itp new file mode 100644 index 0000000..d2edb3f --- /dev/null +++ b/tests/data/CHARMM_PNIPAM_extend.itp @@ -0,0 +1,302 @@ +[ atoms ] +; nr type resnr residue atom cgnr charge mass typeB chargeB massB +; residue 1 PNI rtp PNI q +0.0 + 1 CG331 1 PNI C1 1 -0.273 12.011 ; qtot -0.273 + 2 CG321 1 PNI C2 2 -0.191 12.011 ; qtot -0.191 + 3 CG321 1 PNI C3 3 -0.247 12.011 ; qtot -0.247 + 4 CG311 1 PNI C4 4 0.133 12.011 ; qtot 0.133 + 5 CG321 1 PNI C5 5 -0.223 12.011 ; qtot -0.223 + 6 CG331 1 PNI C6 6 -0.303 12.011 ; qtot -0.303 + 7 CG2O1 1 PNI C7 7 0.507 12.011 ; qtot 0.507 + 8 OG2D1 1 PNI O8 8 -0.517 15.9994 ; qtot -0.517 + 9 NG2S1 1 PNI N9 9 -0.492 14.007 ; qtot -0.492 + 10 CG311 1 PNI C10 10 0.021 12.011 ; qtot 0.021 + 11 CG331 1 PNI C11 11 -0.269 12.011 ; qtot -0.269 + 12 CG331 1 PNI C12 12 -0.269 12.011 ; qtot -0.269 + 13 HGA3 1 PNI H13 13 0.09 1.008 ; qtot 0.09 + 14 HGA3 1 PNI H14 14 0.09 1.008 ; qtot 0.09 + 15 HGA3 1 PNI H15 15 0.09 1.008 ; qtot 0.09 + 16 HGA2 1 PNI H16 16 0.09 1.008 ; qtot 0.09 + 17 HGA2 1 PNI H17 17 0.09 1.008 ; qtot 0.09 + 18 HGA2 1 PNI H18 18 0.09 1.008 ; qtot 0.09 + 19 HGA2 1 PNI H19 19 0.09 1.008 ; qtot 0.09 + 20 HGA1 1 PNI H20 20 0.09 1.008 ; qtot 0.09 + 21 HGA2 1 PNI H21 21 0.09 1.008 ; qtot 0.09 + 22 HGA2 1 PNI H22 22 0.09 1.008 ; qtot 0.09 + 23 HGA3 1 PNI H23 23 0.09 1.008 ; qtot 0.09 + 24 HGA3 1 PNI H24 24 0.09 1.008 ; qtot 0.09 + 25 HGA3 1 PNI H25 25 0.09 1.008 ; qtot 0.09 + 26 HGP1 1 PNI H26 26 0.323 1.008 ; qtot 0.323 + 27 HGA1 1 PNI H27 27 0.09 1.008 ; qtot 0.09 + 28 HGA3 1 PNI H28 28 0.09 1.008 ; qtot 0.09 + 29 HGA3 1 PNI H29 29 0.09 1.008 ; qtot 0.09 + 30 HGA3 1 PNI H30 30 0.09 1.008 ; qtot 0.09 + 31 HGA3 1 PNI H31 31 0.09 1.008 ; qtot 0.09 + 32 HGA3 1 PNI H32 32 0.09 1.008 ; qtot 0.09 + 33 HGA3 1 PNI H33 33 0.09 1.008 ; qtot 0.09 + +[ bonds ] +; ai aj funct c0 c1 c2 c3 + 13 1 1 + 17 2 1 + 16 2 1 + 21 5 1 + 2 1 1 + 2 3 1 + 1 15 1 + 1 14 1 + 24 6 1 + 5 22 1 + 5 6 1 + 5 4 1 + 20 4 1 + 6 23 1 + 6 25 1 + 3 4 1 + 3 18 1 + 3 19 1 + 4 7 1 + 26 9 1 + 7 9 1 + 7 8 1 + 9 10 1 + 28 11 1 + 31 12 1 + 10 11 1 + 10 12 1 + 10 27 1 + 29 11 1 + 33 12 1 + 11 30 1 + 12 32 1 + +[ pairs ] +; ai aj funct c0 c1 c2 c3 + 1 4 1 + 1 18 1 + 1 19 1 + 2 5 1 + 2 7 1 + 2 20 1 + 3 6 1 + 3 8 1 + 3 9 1 + 3 13 1 + 3 14 1 + 3 15 1 + 3 21 1 + 3 22 1 + 4 10 1 + 4 16 1 + 4 17 1 + 4 23 1 + 4 24 1 + 4 25 1 + 4 26 1 + 5 8 1 + 5 9 1 + 5 18 1 + 5 19 1 + 6 7 1 + 6 20 1 + 7 11 1 + 7 12 1 + 7 18 1 + 7 19 1 + 7 21 1 + 7 22 1 + 7 27 1 + 8 10 1 + 8 20 1 + 8 26 1 + 9 20 1 + 9 28 1 + 9 29 1 + 9 30 1 + 9 31 1 + 9 32 1 + 9 33 1 + 11 26 1 + 11 31 1 + 11 32 1 + 11 33 1 + 12 26 1 + 12 28 1 + 12 29 1 + 12 30 1 + 13 16 1 + 13 17 1 + 14 16 1 + 14 17 1 + 15 16 1 + 15 17 1 + 16 18 1 + 16 19 1 + 17 18 1 + 17 19 1 + 18 20 1 + 19 20 1 + 20 21 1 + 20 22 1 + 21 23 1 + 21 24 1 + 21 25 1 + 22 23 1 + 22 24 1 + 22 25 1 + 26 27 1 + 27 28 1 + 27 29 1 + 27 30 1 + 27 31 1 + 27 32 1 + 27 33 1 + +[ angles ] +; ai aj ak funct c0 c1 c2 c3 + 13 1 2 5 + 13 1 15 5 + 13 1 14 5 + 2 1 15 5 + 2 1 14 5 + 15 1 14 5 + 17 2 16 5 + 17 2 1 5 + 17 2 3 5 + 16 2 1 5 + 16 2 3 5 + 1 2 3 5 + 2 3 4 5 + 2 3 18 5 + 2 3 19 5 + 4 3 18 5 + 4 3 19 5 + 18 3 19 5 + 5 4 20 5 + 5 4 3 5 + 5 4 7 5 + 20 4 3 5 + 20 4 7 5 + 3 4 7 5 + 21 5 22 5 + 21 5 6 5 + 21 5 4 5 + 22 5 6 5 + 22 5 4 5 + 6 5 4 5 + 24 6 5 5 + 24 6 23 5 + 24 6 25 5 + 5 6 23 5 + 5 6 25 5 + 23 6 25 5 + 4 7 9 5 + 4 7 8 5 + 9 7 8 5 + 26 9 7 5 + 26 9 10 5 + 7 9 10 5 + 9 10 11 5 + 9 10 12 5 + 9 10 27 5 + 11 10 12 5 + 11 10 27 5 + 12 10 27 5 + 28 11 10 5 + 28 11 29 5 + 28 11 30 5 + 10 11 29 5 + 10 11 30 5 + 29 11 30 5 + 31 12 10 5 + 31 12 33 5 + 31 12 32 5 + 10 12 33 5 + 10 12 32 5 + 33 12 32 5 + +[ dihedrals ] +; ai aj ak al funct c0 c1 c2 c3 c4 c5 + 17 2 1 13 9 + 17 2 1 15 9 + 17 2 1 14 9 + 16 2 1 13 9 + 16 2 1 15 9 + 16 2 1 14 9 + 3 2 1 13 9 + 3 2 1 15 9 + 3 2 1 14 9 + 17 2 3 4 9 + 17 2 3 18 9 + 17 2 3 19 9 + 16 2 3 4 9 + 16 2 3 18 9 + 16 2 3 19 9 + 1 2 3 4 9 + 1 2 3 18 9 + 1 2 3 19 9 + 21 5 6 24 9 + 21 5 6 23 9 + 21 5 6 25 9 + 22 5 6 24 9 + 22 5 6 23 9 + 22 5 6 25 9 + 4 5 6 24 9 + 4 5 6 23 9 + 4 5 6 25 9 + 21 5 4 20 9 + 21 5 4 3 9 + 21 5 4 7 9 + 22 5 4 20 9 + 22 5 4 3 9 + 22 5 4 7 9 + 6 5 4 20 9 + 6 5 4 3 9 + 6 5 4 7 9 + 2 3 4 5 9 + 2 3 4 20 9 + 2 3 4 7 9 + 18 3 4 5 9 + 18 3 4 20 9 + 18 3 4 7 9 + 19 3 4 5 9 + 19 3 4 20 9 + 19 3 4 7 9 + 5 4 7 9 9 + 5 4 7 8 9 + 20 4 7 9 9 + 20 4 7 8 9 + 3 4 7 9 9 + 3 4 7 8 9 + 4 7 9 26 9 + 4 7 9 10 9 + 8 7 9 26 9 + 8 7 9 10 9 + 26 9 10 11 9 + 26 9 10 12 9 + 26 9 10 27 9 + 7 9 10 11 9 + 7 9 10 12 9 + 7 9 10 27 9 + 9 10 11 28 9 + 9 10 11 29 9 + 9 10 11 30 9 + 12 10 11 28 9 + 12 10 11 29 9 + 12 10 11 30 9 + 27 10 11 28 9 + 27 10 11 29 9 + 27 10 11 30 9 + 9 10 12 31 9 + 9 10 12 33 9 + 9 10 12 32 9 + 11 10 12 31 9 + 11 10 12 33 9 + 11 10 12 32 9 + 27 10 12 31 9 + 27 10 12 33 9 + 27 10 12 32 9 + +[ dihedrals ] +; ai aj ak al funct c0 c1 c2 c3 c4 c5 + 7 4 9 8 2 diff --git a/tests/data/CHARMM_pnipam_gmx.itp b/tests/data/CHARMM_pnipam_gmx.itp new file mode 100644 index 0000000..ca3fb0d --- /dev/null +++ b/tests/data/CHARMM_pnipam_gmx.itp @@ -0,0 +1,242 @@ +[ atoms ] +; nr type resnr residue atom cgnr charge mass typeB chargeB massB +; residue 1 pni rtp pni q +0.0 + 1 OG2D1 1 pni O1 1 -0.514 15.9994 ; qtot -0.514 + 2 NG2S1 1 pni N2 2 -0.481 14.007 ; qtot -0.481 + 3 CG311 1 pni C3 3 -0.005 12.011 ; qtot -0.005 + 4 CG321 1 pni C4 4 -0.216 12.011 ; qtot -0.216 + 5 CG311 1 pni C5 5 0.021 12.011 ; qtot 0.021 + 6 CG2O1 1 pni C6 6 0.54 12.011 ; qtot 0.54 + 7 CG331 1 pni C7 7 -0.272 12.011 ; qtot -0.272 + 8 CG331 1 pni C8 8 -0.298 12.011 ; qtot -0.298 + 9 CG331 1 pni C9 9 -0.269 12.011 ; qtot -0.269 + 10 CG331 1 pni C10 10 -0.269 12.011 ; qtot -0.269 + 11 HGA1 1 pni H11 11 0.09 1.008 ; qtot 0.09 + 12 HGA2 1 pni H12 12 0.09 1.008 ; qtot 0.09 + 13 HGA2 1 pni H13 13 0.09 1.008 ; qtot 0.09 + 14 HGA1 1 pni H14 14 0.09 1.008 ; qtot 0.09 + 15 HGP1 1 pni H15 15 0.323 1.008 ; qtot 0.323 + 16 HGA3 1 pni H16 16 0.09 1.008 ; qtot 0.09 + 17 HGA3 1 pni H17 17 0.09 1.008 ; qtot 0.09 + 18 HGA3 1 pni H18 18 0.09 1.008 ; qtot 0.09 + 19 HGA3 1 pni H19 19 0.09 1.008 ; qtot 0.09 + 20 HGA3 1 pni H20 20 0.09 1.008 ; qtot 0.09 + 21 HGA3 1 pni H21 21 0.09 1.008 ; qtot 0.09 + 22 HGA3 1 pni H22 22 0.09 1.008 ; qtot 0.09 + 23 HGA3 1 pni H23 23 0.09 1.008 ; qtot 0.09 + 24 HGA3 1 pni H24 24 0.09 1.008 ; qtot 0.09 + 25 HGA3 1 pni H25 25 0.09 1.008 ; qtot 0.09 + 26 HGA3 1 pni H26 26 0.09 1.008 ; qtot 0.09 + 27 HGA3 1 pni H27 27 0.09 1.008 ; qtot 0.09 + +[ bonds ] +; ai aj funct c0 c1 c2 c3 + 1 6 1 + 2 5 1 + 2 6 1 + 2 15 1 + 3 4 1 + 3 6 1 + 3 7 1 + 3 11 1 + 4 8 1 + 4 12 1 + 4 13 1 + 5 9 1 + 5 10 1 + 5 14 1 + 7 16 1 + 7 17 1 + 7 18 1 + 8 19 1 + 8 20 1 + 8 21 1 + 9 22 1 + 9 23 1 + 9 24 1 + 10 25 1 + 10 26 1 + 10 27 1 + +[ pairs ] +; ai aj funct c0 c1 c2 c3 + 1 4 1 + 1 5 1 + 1 7 1 + 1 11 1 + 1 15 1 + 2 4 1 + 2 7 1 + 2 11 1 + 2 22 1 + 2 23 1 + 2 24 1 + 2 25 1 + 2 26 1 + 2 27 1 + 3 5 1 + 3 15 1 + 3 19 1 + 3 20 1 + 3 21 1 + 4 16 1 + 4 17 1 + 4 18 1 + 6 8 1 + 6 9 1 + 6 10 1 + 6 12 1 + 6 13 1 + 6 14 1 + 6 16 1 + 6 17 1 + 6 18 1 + 7 8 1 + 7 12 1 + 7 13 1 + 8 11 1 + 9 15 1 + 9 25 1 + 9 26 1 + 9 27 1 + 10 15 1 + 10 22 1 + 10 23 1 + 10 24 1 + 11 12 1 + 11 13 1 + 11 16 1 + 11 17 1 + 11 18 1 + 12 19 1 + 12 20 1 + 12 21 1 + 13 19 1 + 13 20 1 + 13 21 1 + 14 15 1 + 14 22 1 + 14 23 1 + 14 24 1 + 14 25 1 + 14 26 1 + 14 27 1 + +[ angles ] +; ai aj ak funct c0 c1 c2 c3 + 5 2 6 5 + 5 2 15 5 + 6 2 15 5 + 4 3 6 5 + 4 3 7 5 + 4 3 11 5 + 6 3 7 5 + 6 3 11 5 + 7 3 11 5 + 3 4 8 5 + 3 4 12 5 + 3 4 13 5 + 8 4 12 5 + 8 4 13 5 + 12 4 13 5 + 2 5 9 5 + 2 5 10 5 + 2 5 14 5 + 9 5 10 5 + 9 5 14 5 + 10 5 14 5 + 1 6 2 5 + 1 6 3 5 + 2 6 3 5 + 3 7 16 5 + 3 7 17 5 + 3 7 18 5 + 16 7 17 5 + 16 7 18 5 + 17 7 18 5 + 4 8 19 5 + 4 8 20 5 + 4 8 21 5 + 19 8 20 5 + 19 8 21 5 + 20 8 21 5 + 5 9 22 5 + 5 9 23 5 + 5 9 24 5 + 22 9 23 5 + 22 9 24 5 + 23 9 24 5 + 5 10 25 5 + 5 10 26 5 + 5 10 27 5 + 25 10 26 5 + 25 10 27 5 + 26 10 27 5 + +[ dihedrals ] +; ai aj ak al funct c0 c1 c2 c3 c4 c5 + 6 2 5 9 9 + 6 2 5 10 9 + 6 2 5 14 9 + 15 2 5 9 9 + 15 2 5 10 9 + 15 2 5 14 9 + 5 2 6 1 9 + 5 2 6 3 9 + 15 2 6 1 9 + 15 2 6 3 9 + 6 3 4 8 9 + 6 3 4 12 9 + 6 3 4 13 9 + 7 3 4 8 9 + 7 3 4 12 9 + 7 3 4 13 9 + 11 3 4 8 9 + 11 3 4 12 9 + 11 3 4 13 9 + 4 3 6 1 9 + 4 3 6 2 9 + 7 3 6 1 9 + 7 3 6 2 9 + 11 3 6 1 9 + 11 3 6 2 9 + 4 3 7 16 9 + 4 3 7 17 9 + 4 3 7 18 9 + 6 3 7 16 9 + 6 3 7 17 9 + 6 3 7 18 9 + 11 3 7 16 9 + 11 3 7 17 9 + 11 3 7 18 9 + 3 4 8 19 9 + 3 4 8 20 9 + 3 4 8 21 9 + 12 4 8 19 9 + 12 4 8 20 9 + 12 4 8 21 9 + 13 4 8 19 9 + 13 4 8 20 9 + 13 4 8 21 9 + 2 5 9 22 9 + 2 5 9 23 9 + 2 5 9 24 9 + 10 5 9 22 9 + 10 5 9 23 9 + 10 5 9 24 9 + 14 5 9 22 9 + 14 5 9 23 9 + 14 5 9 24 9 + 2 5 10 25 9 + 2 5 10 26 9 + 2 5 10 27 9 + 9 5 10 25 9 + 9 5 10 26 9 + 9 5 10 27 9 + 14 5 10 25 9 + 14 5 10 26 9 + 14 5 10 27 9 + +[ dihedrals ] +; ai aj ak al funct c0 c1 c2 c3 c4 c5 + 6 3 2 1 2 \ No newline at end of file diff --git a/tests/data/OPLS_UNK_460A12.itp b/tests/data/OPLS_UNK_460A12.itp new file mode 100644 index 0000000..28860e9 --- /dev/null +++ b/tests/data/OPLS_UNK_460A12.itp @@ -0,0 +1,301 @@ +[ atoms ] +; nr type resnr residue atom cgnr charge mass + 1 opls_800 1 UNK C00 1 -0.2389 12.0110 + 2 opls_801 1 UNK C01 1 -0.1779 12.0110 + 3 opls_802 1 UNK C02 1 -0.1660 12.0110 + 4 opls_803 1 UNK C03 1 -0.1329 12.0110 + 5 opls_804 1 UNK C04 1 -0.1639 12.0110 + 6 opls_805 1 UNK C05 1 -0.2400 12.0110 + 7 opls_806 1 UNK C06 1 0.6111 12.0110 + 8 opls_807 1 UNK O07 1 -0.4483 15.9990 + 9 opls_808 1 UNK N08 1 -1.1135 14.0070 + 10 opls_809 1 UNK C09 1 0.2101 12.0110 + 11 opls_810 1 UNK C0A 1 -0.2525 12.0110 + 12 opls_811 1 UNK C0B 1 -0.2621 12.0110 + 13 opls_812 1 UNK H0C 1 0.0828 1.0080 + 14 opls_813 1 UNK H0D 1 0.0828 1.0080 + 15 opls_814 1 UNK H0E 1 0.0828 1.0080 + 16 opls_815 1 UNK H0F 1 0.0871 1.0080 + 17 opls_816 1 UNK H0G 1 0.0871 1.0080 + 18 opls_817 1 UNK H0H 1 0.1074 1.0080 + 19 opls_818 1 UNK H0I 1 0.1074 1.0080 + 20 opls_819 1 UNK H0J 1 0.1054 1.0080 + 21 opls_820 1 UNK H0K 1 0.0888 1.0080 + 22 opls_821 1 UNK H0M 1 0.0888 1.0080 + 23 opls_822 1 UNK H0N 1 0.0886 1.0080 + 24 opls_823 1 UNK H0O 1 0.0886 1.0080 + 25 opls_824 1 UNK H0P 1 0.0886 1.0080 + 26 opls_825 1 UNK H0Q 1 0.5084 1.0080 + 27 opls_826 1 UNK H0R 1 0.1356 1.0080 + 28 opls_827 1 UNK H0S 1 0.0906 1.0080 + 29 opls_828 1 UNK H0T 1 0.0906 1.0080 + 30 opls_829 1 UNK H0U 1 0.0906 1.0080 + 31 opls_830 1 UNK H0V 1 0.0908 1.0080 + 32 opls_831 1 UNK H0W 1 0.0908 1.0080 + 33 opls_832 1 UNK H0X 2 0.0908 1.0080 +[ bonds ] + 2 1 1 0.1529 224262.400 + 3 2 1 0.1529 224262.400 + 4 3 1 0.1529 224262.400 + 5 4 1 0.1529 224262.400 + 6 5 1 0.1529 224262.400 + 7 4 1 0.1522 265265.600 + 8 7 1 0.1229 476976.000 + 9 7 1 0.1335 410032.000 + 10 9 1 0.1449 282001.600 + 11 10 1 0.1529 224262.400 + 12 10 1 0.1529 224262.400 + 13 1 1 0.1090 284512.000 + 14 1 1 0.1090 284512.000 + 15 1 1 0.1090 284512.000 + 16 2 1 0.1090 284512.000 + 17 2 1 0.1090 284512.000 + 18 3 1 0.1090 284512.000 + 19 3 1 0.1090 284512.000 + 20 4 1 0.1090 284512.000 + 21 5 1 0.1090 284512.000 + 22 5 1 0.1090 284512.000 + 23 6 1 0.1090 284512.000 + 24 6 1 0.1090 284512.000 + 25 6 1 0.1090 284512.000 + 26 9 1 0.1010 363171.200 + 27 10 1 0.1090 284512.000 + 28 11 1 0.1090 284512.000 + 29 11 1 0.1090 284512.000 + 30 11 1 0.1090 284512.000 + 31 12 1 0.1090 284512.000 + 32 12 1 0.1090 284512.000 + 33 12 1 0.1090 284512.000 + +[ angles ] +; ai aj ak funct c0 c1 c2 c3 + 1 2 3 1 112.700 488.273 + 2 3 4 1 112.700 488.273 + 3 4 5 1 112.700 488.273 + 4 5 6 1 112.700 488.273 + 3 4 7 1 111.100 527.184 + 4 7 8 1 120.400 669.440 + 4 7 9 1 116.600 585.760 + 7 9 10 1 121.900 418.400 + 9 10 11 1 109.700 669.440 + 9 10 12 1 109.700 669.440 + 2 1 13 1 110.700 313.800 + 2 1 14 1 110.700 313.800 + 2 1 15 1 110.700 313.800 + 1 2 16 1 110.700 313.800 + 1 2 17 1 110.700 313.800 + 2 3 18 1 110.700 313.800 + 2 3 19 1 110.700 313.800 + 3 4 20 1 110.700 313.800 + 4 5 21 1 110.700 313.800 + 4 5 22 1 110.700 313.800 + 5 6 23 1 110.700 313.800 + 5 6 24 1 110.700 313.800 + 5 6 25 1 110.700 313.800 + 7 9 26 1 119.800 292.880 + 9 10 27 1 109.500 292.880 + 10 11 28 1 110.700 313.800 + 10 11 29 1 110.700 313.800 + 10 11 30 1 110.700 313.800 + 10 12 31 1 110.700 313.800 + 10 12 32 1 110.700 313.800 + 10 12 33 1 110.700 313.800 + 11 10 12 1 112.700 488.273 + 11 10 27 1 110.700 313.800 + 31 12 33 1 107.800 276.144 + 13 1 14 1 107.800 276.144 + 5 4 7 1 111.100 527.184 + 31 12 32 1 107.800 276.144 + 6 5 22 1 110.700 313.800 + 21 5 22 1 107.800 276.144 + 3 2 17 1 110.700 313.800 + 12 10 27 1 110.700 313.800 + 28 11 29 1 107.800 276.144 + 4 3 19 1 110.700 313.800 + 29 11 30 1 107.800 276.144 + 8 7 9 1 122.900 669.440 + 7 4 20 1 109.500 292.880 + 28 11 30 1 107.800 276.144 + 32 12 33 1 107.800 276.144 + 3 2 16 1 110.700 313.800 + 18 3 19 1 107.800 276.144 + 4 3 18 1 110.700 313.800 + 16 2 17 1 107.800 276.144 + 14 1 15 1 107.800 276.144 + 23 6 24 1 107.800 276.144 + 6 5 21 1 110.700 313.800 + 5 4 20 1 110.700 313.800 + 10 9 26 1 118.400 317.984 + 24 6 25 1 107.800 276.144 + 23 6 25 1 107.800 276.144 + 13 1 15 1 107.800 276.144 + +[ dihedrals ] +; IMPROPER DIHEDRAL ANGLES +; ai aj ak al funct c0 c1 c2 c3 c4 c5 + 26 9 7 10 4 180.000 10.460 2 + 9 7 4 8 4 180.000 43.932 2 + +[ dihedrals ] +; PROPER DIHEDRAL ANGLES +; ai aj ak al funct c0 c1 c2 c3 c4 c5 + 7 4 5 6 3 -4.960 6.286 1.310 -2.636 -0.000 0.000 + 7 4 3 2 3 -4.960 6.286 1.310 -2.636 -0.000 0.000 + 4 3 2 1 3 2.301 -1.464 0.837 -1.674 -0.000 0.000 + 5 4 3 2 3 2.301 -1.464 0.837 -1.674 -0.000 0.000 + 6 5 4 3 3 2.301 -1.464 0.837 -1.674 -0.000 0.000 + 11 10 9 7 3 1.933 0.000 -1.933 -0.000 -0.000 0.000 + 12 10 9 7 3 1.933 0.000 -1.933 -0.000 -0.000 0.000 + 10 9 7 4 3 30.288 -4.812 -25.476 -0.000 -0.000 0.000 + 10 9 7 8 3 25.476 0.000 -25.476 -0.000 -0.000 0.000 + 26 9 7 4 3 20.502 0.000 -20.502 -0.000 -0.000 0.000 + 26 9 7 8 3 20.502 0.000 -20.502 -0.000 -0.000 0.000 + 26 9 10 11 3 0.000 0.000 0.000 -0.000 -0.000 0.000 + 26 9 10 12 3 0.000 0.000 0.000 -0.000 -0.000 0.000 + 20 4 7 9 3 0.000 0.000 0.000 -0.000 -0.000 0.000 + 20 4 7 8 3 0.000 0.000 0.000 -0.000 -0.000 0.000 + 22 5 4 7 3 -0.209 -0.628 0.000 0.837 -0.000 0.000 + 19 3 4 7 3 -0.209 -0.628 0.000 0.837 -0.000 0.000 + 18 3 4 7 3 -0.209 -0.628 0.000 0.837 -0.000 0.000 + 21 5 4 7 3 -0.209 -0.628 0.000 0.837 -0.000 0.000 + 30 11 10 12 3 0.628 1.883 0.000 -2.510 -0.000 0.000 + 15 1 2 3 3 0.628 1.883 0.000 -2.510 -0.000 0.000 + 29 11 10 12 3 0.628 1.883 0.000 -2.510 -0.000 0.000 + 22 5 4 3 3 0.628 1.883 0.000 -2.510 -0.000 0.000 + 24 6 5 4 3 0.628 1.883 0.000 -2.510 -0.000 0.000 + 32 12 10 11 3 0.628 1.883 0.000 -2.510 -0.000 0.000 + 14 1 2 3 3 0.628 1.883 0.000 -2.510 -0.000 0.000 + 31 12 10 11 3 0.628 1.883 0.000 -2.510 -0.000 0.000 + 20 4 5 6 3 0.628 1.883 0.000 -2.510 -0.000 0.000 + 17 2 3 4 3 0.628 1.883 0.000 -2.510 -0.000 0.000 + 19 3 4 5 3 0.628 1.883 0.000 -2.510 -0.000 0.000 + 19 3 2 1 3 0.628 1.883 0.000 -2.510 -0.000 0.000 + 20 4 3 2 3 0.628 1.883 0.000 -2.510 -0.000 0.000 + 33 12 10 11 3 0.628 1.883 0.000 -2.510 -0.000 0.000 + 18 3 4 5 3 0.628 1.883 0.000 -2.510 -0.000 0.000 + 23 6 5 4 3 0.628 1.883 0.000 -2.510 -0.000 0.000 + 18 3 2 1 3 0.628 1.883 0.000 -2.510 -0.000 0.000 + 13 1 2 3 3 0.628 1.883 0.000 -2.510 -0.000 0.000 + 21 5 4 3 3 0.628 1.883 0.000 -2.510 -0.000 0.000 + 28 11 10 12 3 0.628 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1.883 0.000 -2.510 -0.000 0.000 + 21 5 4 20 3 0.628 1.883 0.000 -2.510 -0.000 0.000 + 19 3 2 17 3 0.628 1.883 0.000 -2.510 -0.000 0.000 + 20 4 3 18 3 0.628 1.883 0.000 -2.510 -0.000 0.000 + 23 6 5 21 3 0.628 1.883 0.000 -2.510 -0.000 0.000 + 22 5 4 20 3 0.628 1.883 0.000 -2.510 -0.000 0.000 + 24 6 5 22 3 0.628 1.883 0.000 -2.510 -0.000 0.000 + 17 2 1 15 3 0.628 1.883 0.000 -2.510 -0.000 0.000 + 16 2 1 13 3 0.628 1.883 0.000 -2.510 -0.000 0.000 + 32 12 10 27 3 0.628 1.883 0.000 -2.510 -0.000 0.000 + 33 12 10 9 3 0.971 2.912 0.000 -3.883 -0.000 0.000 + 31 12 10 9 3 0.971 2.912 0.000 -3.883 -0.000 0.000 + 28 11 10 9 3 0.971 2.912 0.000 -3.883 -0.000 0.000 + 32 12 10 9 3 0.971 2.912 0.000 -3.883 -0.000 0.000 + 29 11 10 9 3 0.971 2.912 0.000 -3.883 -0.000 0.000 + 30 11 10 9 3 0.971 2.912 0.000 -3.883 -0.000 0.000 + 27 10 9 7 3 0.000 0.000 0.000 -0.000 -0.000 0.000 + 27 10 9 26 3 0.000 0.000 0.000 -0.000 -0.000 0.000 + 9 7 4 3 3 0.734 -9.985 -0.791 10.042 -0.000 0.000 + 9 7 4 5 3 0.734 -9.985 -0.791 10.042 -0.000 0.000 + 8 7 4 5 3 0.000 0.000 0.000 -0.000 -0.000 0.000 + 8 7 4 3 3 0.000 0.000 0.000 -0.000 -0.000 0.000 + +[ pairs ] + 1 4 1 + 2 5 1 + 3 6 1 + 2 7 1 + 3 8 1 + 3 9 1 + 6 7 1 + 5 8 1 + 5 9 1 + 4 10 1 + 3 13 1 + 3 14 1 + 8 10 1 + 7 11 1 + 3 15 1 + 7 12 1 + 1 18 1 + 4 16 1 + 1 19 1 + 4 17 1 + 2 20 1 + 5 18 1 + 5 19 1 + 3 21 1 + 7 18 1 + 3 22 1 + 7 19 1 + 6 20 1 + 4 23 1 + 8 20 1 + 7 21 1 + 4 24 1 + 13 16 1 + 9 20 1 + 7 22 1 + 4 25 1 + 14 16 1 + 13 17 1 + 4 26 1 + 15 16 1 + 14 17 1 + 15 17 1 + 16 18 1 + 8 26 1 + 7 27 1 + 17 18 1 + 16 19 1 + 17 19 1 + 11 26 1 + 9 28 1 + 18 20 1 + 12 26 1 + 9 29 1 + 19 20 1 + 9 30 1 + 12 28 1 + 9 31 1 + 20 21 1 + 12 29 1 + 9 32 1 + 20 22 1 + 12 30 1 + 11 31 1 + 9 33 1 + 11 32 1 + 21 23 1 + 11 33 1 + 22 23 1 + 21 24 1 + 22 24 1 + 21 25 1 + 22 25 1 + 26 27 1 + 27 28 1 + 27 29 1 + 27 30 1 + 27 31 1 + 27 32 1 + 27 33 1 diff --git a/tests/polytop/test_polymer.py b/tests/polytop/test_polymer.py index f59de57..681a840 100644 --- a/tests/polytop/test_polymer.py +++ b/tests/polytop/test_polymer.py @@ -235,3 +235,84 @@ def test_multijoined_polymer(data_dir: Path, output_dir: Path): polymer_topology = polymer.topology polymer_topology.to_ITP(output_dir/'double_sugar_polymer.itp') Visualize.polymer(polymer,infer_bond_order=False).draw2D(output_dir/'double_sugar_polymer.png',(400,200)) + +def test_OPLS_polymer(data_dir: Path, output_dir: Path): + """ + This test is to make sure a Polymer constructed from OPLS ff monomers + extends without error + """ + top = Topology.from_ITP(data_dir/"OPLS_UNK_460A12.itp", format="opls") + + # Create a Junction to join 'to' and another to join 'from'. + # Provide the bonding atom and the leaving atom, in that order, for the + # Junction - they must have a bond between them. + to_j = Junction(top.get_atom("C02"), top.get_atom("C01"), name = "to") + from_j = Junction(top.get_atom("C03"), top.get_atom("C04"), name = "from") + + # Create a Monomer from the Topology and a list of the Junctions + monomer = Monomer(top, [to_j, from_j]) + + # Start the Polymer with one Monomer + polymer = Polymer(monomer) + + # Extend the Polymer to the desired length (in this case 20) + for i in range(29): + polymer.extend(monomer, from_junction_name="from", to_junction_name="to") + + # Save the polymer to a file and visualise the structure with RDKit for an easy visual structure check + polymer.topology.to_ITP(output_dir/'OPLS_30mer.itp') + Visualize.polymer(polymer,infer_bond_order=False).draw2D(output_dir/'OPLS_30mer.png',(400,300)) + +def test_AMBER_polymer(data_dir: Path, output_dir: Path): + """ + This test is to make sure a Polymer constructed from AMBER ff monomers + extends without error + """ + top = Topology.from_ITP(data_dir/"AMBER_PNIPAM_extend.itp", format="amber") + + # Create a Junction to join 'to' and another to join 'from'. + # Provide the bonding atom and the leaving atom, in that order, for the + # Junction - they must have a bond between them. + to_j = Junction(top.get_atom("C02"), top.get_atom("C01"), name = "to") + from_j = Junction(top.get_atom("C03"), top.get_atom("C04"), name = "from") + + # Create a Monomer from the Topology and a list of the Junctions + monomer = Monomer(top, [to_j, from_j]) + + # Start the Polymer with one Monomer + polymer = Polymer(monomer) + + # Extend the Polymer to the desired length (in this case 20) + for i in range(29): + polymer.extend(monomer, from_junction_name="from", to_junction_name="to") + + # Save the polymer to a file and visualise the structure with RDKit for an easy visual structure check + polymer.topology.to_ITP(output_dir/'AMBER_30mer.itp') + Visualize.polymer(polymer,infer_bond_order=False).draw2D(output_dir/'AMBER_30mer.png',(400,300)) + +def test_CHARMM_polymer(data_dir: Path, output_dir: Path): + """ + This test is to make sure a Polymer constructed from CHARMM ff monomers + extends without error + """ + top = Topology.from_ITP(data_dir/"CHARMM_PNIPAM_extend.itp", format="charmm") + + # Create a Junction to join 'to' and another to join 'from'. + # Provide the bonding atom and the leaving atom, in that order, for the + # Junction - they must have a bond between them. + to_j = Junction(top.get_atom("C2"), top.get_atom("C1"), name = "to") + from_j = Junction(top.get_atom("C3"), top.get_atom("C4"), name = "from") + + # Create a Monomer from the Topology and a list of the Junctions + monomer = Monomer(top, [to_j, from_j]) + + # Start the Polymer with one Monomer + polymer = Polymer(monomer) + + # Extend the Polymer to the desired length (in this case 20) + for i in range(29): + polymer.extend(monomer, from_junction_name="from", to_junction_name="to") + + # Save the polymer to a file and visualise the structure with RDKit for an easy visual structure check + polymer.topology.to_ITP(output_dir/'CHARMM_30mer.itp') + Visualize.polymer(polymer,infer_bond_order=False).draw2D(output_dir/'CHARMM_30mer.png',(400,300)) \ No newline at end of file diff --git a/tests/polytop/test_topology.py b/tests/polytop/test_topology.py index 4906e41..0ac94c2 100644 --- a/tests/polytop/test_topology.py +++ b/tests/polytop/test_topology.py @@ -129,6 +129,106 @@ def test_topology_auto_rename_atoms(data_dir: Path, output_dir: Path): assert arg_max_atom_index["N"] == 4 assert arg_max_atom_index["O"] == 2 +def test_topology_bad_format_parser(data_dir: Path, output_dir: Path): + with pytest.raises(ValueError): + check = Topology.from_ITP(data_dir/"OPLS_UNK_460A12.itp", format="pls") + +def test_topology_OPLS_parser(data_dir: Path, output_dir: Path): + opls = Topology.from_ITP(data_dir/"OPLS_UNK_460A12.itp", format="opls") + opls.to_ITP(output_dir/"OPLS_topology.itp") + opls_new = Topology.from_ITP(output_dir/"OPLS_topology.itp", format="opls") + + def same_properties(atom_a, atom_b)-> bool: + if atom_a.atom_type != atom_b.atom_type: + return False + if atom_a.residue_name != atom_b.residue_name: + return False + if atom_a.residue_id != atom_b.residue_id: + return False + if atom_a.partial_charge != atom_b.partial_charge: + return False + if atom_a.mass != atom_b.mass: + return False + return True + + atoms = opls.atoms + new_atoms = opls_new.atoms + assert len(atoms) == len(new_atoms) + for i in range(len(atoms)): + atom = atoms[i] + new_atom = new_atoms[i] + assert same_properties(atom, new_atom) + for a in atom.bond_neighbours(): + assert any(same_properties(a, new_a) for new_a in new_atom.bond_neighbours()) + for a in atom.angle_neighbours(): + assert any(same_properties(a, new_a) for new_a in new_atom.angle_neighbours()) + for a in atom.dihedral_neighbours(): + assert any(same_properties(a, new_a) for new_a in new_atom.dihedral_neighbours()) + +def test_topology_CHARMM_parser(data_dir: Path, output_dir: Path): + charmm = Topology.from_ITP(data_dir/"CHARMM_pnipam_gmx.itp", format="charmm") + charmm.to_ITP(output_dir/"CHARMM_topology.itp") + charmm_new = Topology.from_ITP(output_dir/"CHARMM_topology.itp", format="charmm") + + def same_properties(atom_a, atom_b)-> bool: + if atom_a.atom_type != atom_b.atom_type: + return False + if atom_a.residue_name != atom_b.residue_name: + return False + if atom_a.residue_id != atom_b.residue_id: + return False + if atom_a.partial_charge != atom_b.partial_charge: + return False + if atom_a.mass != atom_b.mass: + return False + return True + + atoms = charmm.atoms + new_atoms = charmm_new.atoms + assert len(atoms) == len(new_atoms) + for i in range(len(atoms)): + atom = atoms[i] + new_atom = new_atoms[i] + assert same_properties(atom, new_atom) + for a in atom.bond_neighbours(): + assert any(same_properties(a, new_a) for new_a in new_atom.bond_neighbours()) + for a in atom.angle_neighbours(): + assert any(same_properties(a, new_a) for new_a in new_atom.angle_neighbours()) + for a in atom.dihedral_neighbours(): + assert any(same_properties(a, new_a) for new_a in new_atom.dihedral_neighbours()) + +def test_topology_AMBER_parser(data_dir: Path, output_dir: Path): + amber = Topology.from_ITP(data_dir/"AMBER_pnipam_GMX.itp", format="amber") + amber.to_ITP(output_dir/"AMBER_topology.itp") + amber_new = Topology.from_ITP(output_dir/"AMBER_topology.itp", format="amber") + + def same_properties(atom_a, atom_b)-> bool: + if atom_a.atom_type != atom_b.atom_type: + return False + if atom_a.residue_name != atom_b.residue_name: + return False + if atom_a.residue_id != atom_b.residue_id: + return False + if atom_a.partial_charge != atom_b.partial_charge: + return False + if atom_a.mass != atom_b.mass: + return False + return True + + atoms = amber.atoms + new_atoms = amber_new.atoms + assert len(atoms) == len(new_atoms) + for i in range(len(atoms)): + atom = atoms[i] + new_atom = new_atoms[i] + assert same_properties(atom, new_atom) + for a in atom.bond_neighbours(): + assert any(same_properties(a, new_a) for new_a in new_atom.bond_neighbours()) + for a in atom.angle_neighbours(): + assert any(same_properties(a, new_a) for new_a in new_atom.angle_neighbours()) + for a in atom.dihedral_neighbours(): + assert any(same_properties(a, new_a) for new_a in new_atom.dihedral_neighbours()) + @pytest.mark.xfail(reason="New method of separating atoms into unique charge groups and renumbering them before saving to ITP is breaking this test.") def test_reverse_topology(data_dir: Path, output_dir: Path): glu = Topology.from_ITP(data_dir/"glutamine.itp")