On 8/31/15 4:03 AM, Alex Cullen wrote:
Dear gmx-users, I am simulating a polymer, and I am really beginner in this area. when I execute pdb2gmx command I get posre.itp, topol.top, and conf.gro files, but there are no bonded, angles, and dihedral interactions in the topology file, only atoms and their chrges for each residue!
Then you haven't added any [bonds] in the .rtp file. Without these, no bonded interactions can be generated.
-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.
