On 1/8/16 5:46 AM, 张敏华 wrote:
Hi everyone, I encountered a problem when I using pdb2gmx to convert a pdb file into gro and top file. The system give me a fatal error message as following: Fatal error: Residue 145 named LYS of a molecule in the input file was mapped to an entry in the topology database, but the atom CG used in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. But the 145 residue is LEU actually, and the sidechain of this residue is OK, I replaced this residue with ALA, ARG or LYS but the error message remains. So does anyone know the cause and help me to solve this ?
pdb2gmx uses its own internal residue numbering. You must have a lysine somewhere with an incomplete side chain (a very common problem). You'll need to fix the structure using e.g. SwissPDBViewer or some other modeling software before running the structure through pdb2gmx.
-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.
