Hi, Please stop doing that. You're risking wasting your own time as well. ;-)
Mark On Tue, Jul 11, 2017 at 11:52 PM Alex <nedoma...@gmail.com> wrote: > You are absolutely right once again. I've been glancing over that topology, > looking right at what the problem was, and not seeing it. The residue name > column was empty, all atom types went to crap, but because I always grompp > with -maxwarn 10 (for completely unrelated warnings in completely different > simulations) everything seemed okay. > > Thanks! > > Alex > > On Tue, Jul 11, 2017 at 2:40 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > > > > > On 7/11/17 4:01 PM, Alex wrote: > > > >> Hi all, > >> > >> I have a tiny acetonitrile molecule here. The input pdb prior to EM is > >> this: > >> > >> TITLE Gromacs Runs On Most of All Computer Systems > >> REMARK THIS IS A SIMULATION BOX > >> CRYST1 30.000 30.000 30.000 90.00 90.00 90.00 P 1 > >> MODEL 1 > >> ATOM 1 CT ACT 1 14.870 14.744 14.594 1.00 0.00 > >> C > >> ATOM 2 HC ACT 1 15.390 13.760 14.594 1.00 0.00 > >> H > >> ATOM 3 HC ACT 1 13.769 14.581 14.594 1.00 0.00 > >> H > >> ATOM 4 HC ACT 1 15.162 15.317 13.685 1.00 0.00 > >> H > >> ATOM 5 CZ ACT 1 15.253 15.501 15.794 1.00 0.00 > >> C > >> ATOM 6 NZ ACT 1 15.555 16.097 16.740 1.00 0.00 > >> N > >> TER > >> ENDMDL > >> > >> The output, however, is this: > >> > >> TITLE Great Red Owns Many ACres of Sand > >> REMARK THIS IS A SIMULATION BOX > >> CRYST1 30.000 30.000 30.000 90.00 90.00 90.00 P 1 1 > >> MODEL 1 > >> ATOM 1 1 CT 1 15.013 15.013 14.819 1.00 0.00 > >> C > >> ATOM 2 1 HC 1 14.952 13.831 14.385 1.00 0.00 > >> H > >> ATOM 3 1 HC 1 13.827 14.934 14.400 1.00 0.00 > >> H > >> ATOM 4 1 HC 1 15.140 15.157 13.573 1.00 0.00 > >> H > >> ATOM 5 2 CZ 1 15.821 15.819 16.308 1.00 0.00 > >> C > >> ATOM 6 2 NZ 1 16.401 16.397 17.446 1.00 0.00 > >> N > >> TER > >> ENDMDL > >> > >> Why? I don't think I've seen this happen before, and I'd like to keep > the > >> initial format. Any suggestions? My itp is for an ACT residue, which is > >> included in the simulation topology input. > >> > >> > > mdrun gets the residue and atom names from the topology, so a dump of the > > .tpr should show something useful. It seems like something in the > topology > > has gotten broken - atom names becoming numbers, residue name becoming > the > > atom names. Bizarre. grompp should have complained loudly if there were > > mismatches between coordinates and topology. > > > > -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. > > > -- > 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.