On 3/30/16 8:16 AM, Brett wrote:
Dear All, When I work with pdb2gmx for force field 54a7, I meet the following "WARNING: Residue 54 named ILE 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". Why you please let me know how to localize the topology database and how to localize ILE in the topology database , so that I can compare the atom O with that in my input pdb file, for fix of my pdb file?
The error is explicit - you are missing an O atom (backbone carbonyl oxygen) in your coordinates. You need to fix any missing atoms or residues.
-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.
