On 5/19/17 6:31 PM, ZHANG Cheng wrote:
Dear Justin, I replied the thread already, but it is waiting for approval due to large email content. Could you please approve it?
I have no control over that. If it's too much for an email (normally pdb2gmx output is fine) then upload to e.g. pastebin and provide the URL.
-Justin
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
-- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- 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.
