On 8/19/16 10:52 AM, amitbe...@chemeng.iisc.ernet.in wrote:
Hello users, I am using pdb2gmx on a protein. Fatal error: Residue 1 named LYS 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. ATOM 1 N LYS 8 59.565 44.696 51.226 1.00 0.00 N 0.00 H ATOM 19 NZ LYS 8 62.201 50.111 51.767 1.00 0.00 N These are N atoms in my LYS . Can anyone point out what the problem.
Please provide your exact pdb2gmx command and the full screen output. -Justin -- ================================================== 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.
