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.
