Thanks for your reply. Anyway, looks like every pdb I convert using above command leads to this warning, for example, when I try with 1TIT: http://www.pdb.org/pdb/explore/explore.do?structureId=1TIT
I also get the same kind of warning while loading generated .gro file, telling me that something is "strange" with the last residue. Maybe gromacs is using a different nomenclature inside the generated .gro file that VMD is failing to understand, but the problem looks to appear in all cases I have tested 2013/12/4 Justin Lemkul <jalem...@vt.edu> > > > On 12/4/13 5:33 AM, Pacho Ramos wrote: > >> When I convert attached .pdb file to .gro using: >> pdb2gmx -quiet -ff amber99 -water none -f ${MOL}.pdb -o ${MOL}Initial.gro >> -i ${MOL}.itp -p ${MOL}.top -ignh >> >> the generated .gro file causes vmd (1.9.1) to show this warning while >> loading it: >> Warning) Unusual bond between residues: 905 (protein) and 906 (none) >> >> Should I wonder about it? Or is pdb2gmx (from gromacs 4.6.2) generating a >> wrong .gro file for some reason? >> >> > What VMD thinks about bonds is irrelevant. See http://www.gromacs.org/ > Downloads/Related_Software/Visualization_Software# > Topology_bonds_vs_Rendered_bonds. > > You have two atoms that are close enough together that VMD guesses there > should be a bond, but the "bond" occurs between chemically distinct > entities, so it warns you. It's not an important message in most cases. > For the purposes of the simulation, the only bonds that matter are the > ones defined in the .top file. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > ================================================== > -- > 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. > -- 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.