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Changes from GROMACS v2019.1 to v2022.2

Pau Andrio edited this page Sep 8, 2022 · 4 revisions

pdb2gmx renames HIS as HISE, HISD or HISP.

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