Dear Justin, I replied the thread already, but it is waiting for approval due to large email content. Could you please approve it?
Cheng ---Original--- From: "ZHANG Cheng"<272699...@qq.com> Date: 2017/5/19 22:37:52 To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; Cc: "????QQ"<272699...@qq.com>; Subject: pdb2gmx: Atom N used in the topology not found in the input (PDB) file Dear Gromacs, I got this fatal error after running "pdb2gmx": Fatal error: Residue 1 named ASP of a molecule in the input file was mapped to an entry in the topology database, but the atom N used in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. However, the residue 1 in the PDB is: ATOM 1 N ASP L 1 24.330 14.711 -3.854 1.00 0.00 N ATOM 2 CA ASP L 1 25.669 15.093 -3.310 1.00 0.00 C ATOM 3 C ASP L 1 25.766 14.899 -1.791 1.00 0.00 C ATOM 4 O ASP L 1 26.581 14.101 -1.318 1.00 0.00 O ATOM 5 CB ASP L 1 25.989 16.552 -3.646 1.00 0.00 C ATOM 6 CG ASP L 1 26.260 16.773 -5.128 1.00 0.00 C ATOM 7 OD1 ASP L 1 26.489 15.809 -5.821 1.00 0.00 O ATOM 8 OD2 ASP L 1 26.236 17.903 -5.554 1.00 0.00 O ATOM 9 1H ASP L 1 24.318 14.855 -4.844 1.00 0.00 H ATOM 10 2H ASP L 1 24.152 13.747 -3.656 1.00 0.00 H ATOM 11 3H ASP L 1 23.623 15.275 -3.427 1.00 0.00 H ATOM 12 HA ASP L 1 26.425 14.456 -3.771 1.00 0.00 H ATOM 13 1HB ASP L 1 25.154 17.186 -3.346 1.00 0.00 H ATOM 14 2HB ASP L 1 26.864 16.873 -3.080 1.00 0.00 H You can see that the first atom is just atom N, not missing. Can I ask why I still got this error? Another mutant file of the protein works totally fine for pdb2gmx. Its 1st residue ASP is the below, I could not see any big difference except slight difference in the coordinates. ATOM 1 N ASP L 1 24.330 14.711 -3.854 1.00 0.00 N ATOM 2 CA ASP L 1 25.669 15.093 -3.310 1.00 0.00 C ATOM 3 C ASP L 1 25.766 14.899 -1.791 1.00 0.00 C ATOM 4 O ASP L 1 26.586 14.106 -1.317 1.00 0.00 O ATOM 5 CB ASP L 1 25.989 16.552 -3.646 1.00 0.00 C ATOM 6 CG ASP L 1 26.260 16.773 -5.128 1.00 0.00 C ATOM 7 OD1 ASP L 1 26.489 15.810 -5.821 1.00 0.00 O ATOM 8 OD2 ASP L 1 26.235 17.904 -5.554 1.00 0.00 O ATOM 9 1H ASP L 1 24.318 14.855 -4.844 1.00 0.00 H ATOM 10 2H ASP L 1 24.152 13.747 -3.656 1.00 0.00 H ATOM 11 3H ASP L 1 23.623 15.275 -3.427 1.00 0.00 H ATOM 12 HA ASP L 1 26.425 14.456 -3.771 1.00 0.00 H ATOM 13 1HB ASP L 1 25.154 17.186 -3.345 1.00 0.00 H ATOM 14 2HB ASP L 1 26.864 16.872 -3.080 1.00 0.00 H Thank you. Yours sincerely Cheng -- 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.
