On 5/6/15 7:55 AM, Urszula Uciechowska wrote:
Hi, I am trying to run pdb2gmx by using: pdb2gmx -f COM-oH.pdb -o COM-oH.gro -p COM-oH.top -ignh -water tip3p -ter however I am getting a fatal error: ------------------------------------------------------- Program pdb2gmx, VERSION 4.5.3 Source code file: pgutil.c, line: 99 Fatal error: Atom C not found in residue seq.nr. 137 while adding atom For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- "(That makes 100 errors; please try again.)" (TeX) I have checkec the 137 AA and there is C atom. The system consist of DNA and 3 protein receptors. I used 6: AMBER99SB-ILDN force field. What is wrong here?
You have a missing atom. Make sure you're looking at the right residue; if you have multiple chains it can be simply in another chain with that residue (and I believe pdb2gmx renumbers the chain internally, anyway).
-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.
