[gmx-users] GROMOS 54a7 mapping warning

[David van der Spoel]

Den 2019-07-31 kl. 15:21, skrev Gselman, Larissa:
> Hallo everyone,
> 
> 
> I want to simulate a peptide with the Gromos 54a7 force field.
Your structure is missing atoms, please fix and rerun without -ignh.
> 
> 
> So, my first command is:
> 
> gmx_mpi pdb2gmx -f Mh.pdb -o Mh_processed.gro -water spce -ignh -inter
> 
> I choose 14 for the Gromos 54a7 ff, then I choose the protonation state the titratable amino acids and for the termini I choose the zwitterionic state (so I choose 0 and 0).
> 
> But this results in the following warnings:
> 
> WARNING: WARNING: Residue 1 named ASP of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed.
> 
> WARNING: WARNING: Residue 38 named ASN of a molecule in the input file was mapped to an entry in the topology database, but the atom O used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed.
> 
> 
> This is the beginning and end of my pdb file with ASP as first and ASN as last amino acid:
> 
> ATOM      1  N   ASP A   1      59.994  60.432  82.286  1.00  7.49
> ATOM      2  CA  ASP A   1      59.341  61.407  81.415  1.00  7.49
> ATOM      3  HA  ASP A   1      58.651  60.833  80.799  1.00  7.49
> ATOM      4  CB  ASP A   1      58.494  62.384  82.263  1.00  7.49
> ATOM      5  HB1 ASP A   1      59.114  63.222  82.584  1.00  7.49
> ATOM      6  HB2 ASP A   1      58.142  61.868  83.157  1.00  7.49
> ATOM      7  CG  ASP A   1      57.247  62.920  81.535  1.00  7.49
> ATOM      8  OD1 ASP A   1      57.107  62.729  80.305  1.00  7.49
> ATOM      9  OD2 ASP A   1      56.369  63.525  82.180  1.00  7.49
> ATOM     10  C   ASP A   1      60.313  62.117  80.435  1.00  7.49
> ATOM     11  O   ASP A   1      61.524  61.881  80.391  1.00  7.49
> .
> .
> .
> ATOM    623  N   ASN A  38      49.792  47.722  37.078  1.00 13.81
> ATOM    624  H   ASN A  38      50.649  48.244  36.922  1.00 13.81
> ATOM    625  CA  ASN A  38      48.636  48.172  36.306  1.00 13.81
> ATOM    626  HA  ASN A  38      48.705  49.256  36.233  1.00 13.81
> ATOM    627  CB  ASN A  38      48.757  47.594  34.881  1.00 13.81
> ATOM    628  HB1 ASN A  38      49.688  47.938  34.433  1.00 13.81
> ATOM    629  HB2 ASN A  38      47.934  47.954  34.264  1.00 13.81
> ATOM    630  CG  ASN A  38      48.756  46.074  34.842  1.00 13.81
> ATOM    631  OD1 ASN A  38      49.775  45.434  34.642  1.00 13.81
> ATOM    632  ND2 ASN A  38      47.621  45.445  35.027  1.00 13.81
> ATOM    633 1HD2 ASN A  38      46.815  45.983  35.313  1.00 13.81
> ATOM    634 2HD2 ASN A  38      47.668  44.445  35.083  1.00 13.81
> ATOM    635  C   ASN A  38      47.283  47.875  36.982  1.00 13.81
> ATOM    636  O   ASN A  38      47.185  47.311  38.072  1.00 13.81
> TER
> 
> 
> I hope you can help me and maybe tell me why this problem occurs and what I have to change. Thank you very much!
> 
> Best regards
> Larissa
> 


-- 
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se