Thank you for your answer! I used the Yasara -> Edit -> Clean Option and it added atoms (1H, 2H and 3H for ASP and OXT for ASN) to my pdb file.
Nevertheless, I still get the same warnings when I try with -ignh. I cannot see that there are other atoms missing? When I try without -ignh, I even get a fatal error which says: Atom HA in residue ASP 1 was not found in rtp entry ASP with 11 atoms while sorting atoms. When I look into the aminoacids.rtp file from the GROMOS 54a7 force field it looks like this: [ ASP ] [ atoms ] N N -0.31000 0 H H 0.31000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG C 0.27000 2 OD1 OM -0.63500 2 OD2 OM -0.63500 2 C C 0.450 3 O O -0.450 3 Here are my first and last amino acids from the new pdb file with the added atoms: ATOM 1 N ASP A 1 59.994 60.432 82.286 1.00 7.49 N ATOM 2 1H ASP A 1 60.547 59.791 81.754 1.00 7.49 H ATOM 3 2H ASP A 1 59.319 59.903 82.801 1.00 7.49 H ATOM 4 3H ASP A 1 60.596 60.885 82.944 1.00 7.49 H ATOM 5 CA ASP A 1 59.341 61.407 81.415 1.00 7.49 C ATOM 6 HA ASP A 1 58.651 60.833 80.799 1.00 7.49 H ATOM 7 C ASP A 1 60.313 62.117 80.435 1.00 7.49 C ATOM 8 O ASP A 1 61.524 61.881 80.391 1.00 7.49 O ATOM 9 CB ASP A 1 58.494 62.384 82.263 1.00 7.49 C ATOM 10 1HB ASP A 1 58.142 61.868 83.157 1.00 7.49 H ATOM 11 2HB ASP A 1 59.114 63.222 82.584 1.00 7.49 H ATOM 12 CG ASP A 1 57.247 62.920 81.535 1.00 7.49 C ATOM 13 OD1 ASP A 1 57.107 62.729 80.305 1.00 7.49 O ATOM 14 OD2 ASP A 1 56.369 63.525 82.180 1.00 7.49 O . . . ATOM 626 N ASN A 38 49.792 47.722 37.078 1.00 13.81 N ATOM 627 H ASN A 38 50.649 48.244 36.922 1.00 13.81 H ATOM 628 CA ASN A 38 48.636 48.172 36.306 1.00 13.81 C ATOM 629 HA ASN A 38 48.705 49.256 36.233 1.00 13.81 H ATOM 630 C ASN A 38 47.283 47.875 36.982 1.00 13.81 C ATOM 631 O ASN A 38 47.185 47.311 38.072 1.00 13.81 O ATOM 632 OXT ASN A 38 46.199 48.179 36.482 1.00 13.81 O ATOM 633 CB ASN A 38 48.757 47.594 34.881 1.00 13.81 C ATOM 634 1HB ASN A 38 47.934 47.954 34.264 1.00 13.81 H ATOM 635 2HB ASN A 38 49.688 47.938 34.433 1.00 13.81 H ATOM 636 CG ASN A 38 48.756 46.074 34.842 1.00 13.81 C ATOM 637 OD1 ASN A 38 49.775 45.434 34.642 1.00 13.81 O ATOM 638 ND2 ASN A 38 47.621 45.445 35.027 1.00 13.81 N ATOM 639 1HD2 ASN A 38 47.668 44.445 35.083 1.00 13.81 H ATOM 640 2HD2 ASN A 38 46.815 45.983 35.313 1.00 13.81 H TER 641 ASN A 38 END Thank you so much for your help. ________________________________ Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> im Auftrag von David van der Spoel <sp...@xray.bmc.uu.se> Gesendet: Mittwoch, 31. Juli 2019 21:21:39 An: gmx-us...@gromacs.org Betreff: Re: [gmx-users] GROMOS 54a7 mapping warning 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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.