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Changes from GROMACS v2019.1 to v2022.2
Pau Andrio edited this page Sep 8, 2022
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4 revisions
pdb2gmx v2019.1 top file extract:
; residue 773 HIS rtp HID q 0.0
1249 N 773 HIS N 1249 -0.4157 14.01
1250 H 773 HIS H 1250 0.2719 1.008
1251 CT 773 HIS CA 1251 0.0188 12.01
1252 H1 773 HIS HA 1252 0.0881 1.008
1253 CT 773 HIS CB 1253 -0.0462 12.01
1254 HC 773 HIS HB1 1254 0.0402 1.008
1255 HC 773 HIS HB2 1255 0.0402 1.008
1256 CC 773 HIS CG 1256 -0.0266 12.01
1257 NA 773 HIS ND1 1257 -0.3811 14.01
1258 H 773 HIS HD1 1258 0.3649 1.008
1259 CR 773 HIS CE1 1259 0.2057 12.01
1260 H5 773 HIS HE1 1260 0.1392 1.008
1261 NB 773 HIS NE2 1261 -0.5727 14.01
1262 CV 773 HIS CD2 1262 0.1292 12.01
1263 H4 773 HIS HD2 1263 0.1147 1.008
1264 C 773 HIS C 1264 0.5973 12.01
1265 O 773 HIS O 1265 -0.5679 16 ; qtot 2
Same top file created using pdb2gmx v2022.2:
; residue 773 HISD rtp HID q 0.0
1249 N 773 HISD N 1249 -0.4157 14.01
1250 H 773 HISD H 1250 0.2719 1.008
1251 CT 773 HISD CA 1251 0.0188 12.01
1252 H1 773 HISD HA 1252 0.0881 1.008
1253 CT 773 HISD CB 1253 -0.0462 12.01
1254 HC 773 HISD HB1 1254 0.0402 1.008
1255 HC 773 HISD HB2 1255 0.0402 1.008
1256 CC 773 HISD CG 1256 -0.0266 12.01
1257 NA 773 HISD ND1 1257 -0.3811 14.01
1258 H 773 HISD HD1 1258 0.3649 1.008
1259 CR 773 HISD CE1 1259 0.2057 12.01
1260 H5 773 HISD HE1 1260 0.1392 1.008
1261 NB 773 HISD NE2 1261 -0.5727 14.01
1262 CV 773 HISD CD2 1262 0.1292 12.01
1263 H4 773 HISD HD2 1263 0.1147 1.008
1264 C 773 HISD C 1264 0.5973 12.01
1265 O 773 HISD O 1265 -0.5679 16 ; qtot 2
Exactly the same happens in the gro file.
pdb2gmx v2019.1 gro file extract:
773HIS N 1249 0.381 8.475 1.799
773HIS H 1250 0.420 8.420 1.874
773HIS CA 1251 0.252 8.441 1.740
773HIS HA 1252 0.243 8.474 1.637
773HIS CB 1253 0.240 8.290 1.721
773HIS HB1 1254 0.137 8.271 1.691
773HIS HB2 1255 0.263 8.245 1.817
773HIS CG 1256 0.325 8.239 1.608
773HIS ND1 1257 0.346 8.296 1.483
773HIS HD1 1258 0.277 8.351 1.434
773HIS CE1 1259 0.461 8.258 1.425
773HIS HE1 1260 0.504 8.278 1.328
773HIS NE2 1261 0.516 8.167 1.506
773HIS CD2 1262 0.438 8.162 1.621
773HIS HD2 1263 0.470 8.108 1.710
773HIS C 1264 0.134 8.506 1.812
773HIS O 1265 0.020 8.462 1.800
Same gro file created using pdb2gmx v2022.2:
773HISD N 1249 0.381 8.475 1.799
773HISD H 1250 0.420 8.420 1.874
773HISD CA 1251 0.252 8.441 1.740
773HISD HA 1252 0.243 8.474 1.637
773HISD CB 1253 0.240 8.290 1.721
773HISD HB1 1254 0.137 8.271 1.691
773HISD HB2 1255 0.263 8.245 1.817
773HISD CG 1256 0.325 8.239 1.608
773HISD ND1 1257 0.346 8.296 1.483
773HISD HD1 1258 0.277 8.351 1.434
773HISD CE1 1259 0.461 8.258 1.425
773HISD HE1 1260 0.504 8.278 1.328
773HISD NE2 1261 0.516 8.167 1.506
773HISD CD2 1262 0.438 8.162 1.621
773HISD HD2 1263 0.470 8.108 1.710
773HISD C 1264 0.134 8.506 1.812
773HISD O 1265 0.020 8.462 1.800