On 11/7/16 10:44 PM, Kingsley Theras Primus Dass . wrote:
Hello users!! I generated a Topology file for SO3- using ATB topology generator , which is compatible with GROMACS. Then I copied the .rtp file from ATB and pasted it into GROMACS aminoacid.rtp. The partial charge of aminoacid sulfated-tyrosine was -1. When I run -pdb2gmx there was error saying the atoms were missing , ------------------------------------------------------- Program gmx pdb2gmx, VERSION 5.1 Source code file: /home/hsulab00/Documents/gromacs-5.1/src/gromacs/gmxpreprocess/pdb2top.cpp, line: 1584 Fatal error: There were 6 missing atoms in molecule Protein_chain_D, if you want to use this incomplete topology anyhow, use the option -missing then I ran pdb2gmx -ignh -p topol.top -missing It generated the topology file. But the parital charge of sulfated tyrosine was changed to -2, coz of missing hydrogen atoms. can you please suggest some solutions , to overcome this problem.
Add an .hdb entry for your residue so that pdb2gmx will build the missing atoms. In general, never use the -missing option.
-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.
