Hallo everyone,
I want to simulate a peptide with the Gromos 54a7 force field. 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 -- 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 [email protected].
