On 8/31/15 11:20 AM, Atsutoshi Okabe wrote:
Hi all, I have a question about how to use inter-molecular bonded interaction tool in GROMACS 5.1. I want to calculate binding free energy between protein and ligand adding harmonic restraint force to prevent the ligand from leaving the binding site when the native ligand-receptor interaction are turned off. So, I added [ intermolecular-interactions ] in complex topology file below. [ molecules ] ; Compound nmols protein 1 CRW 3 ligand 1 SOL 11266 CL 5 [ intermolecular-interactions ] [ bonds ] 411 3173 6 0.55 2090 [ angles ] 411 3173 3152 1 164.5 20.9 409 411 3173 1 122.3 20.9 [ dihedrals ] 409 411 3173 3152 2 12.0 20.9 407 409 411 3173 2 75.6 20.9 411 3173 3152 3144 2 -126.0 20.9 However, I got the following error. Reading file equil1.00.tpr, VERSION 5.1 (single precision) Changing nstlist from 10 to 40, rlist from 1 to 1 Using 8 MPI processes Using 1 OpenMP thread per MPI process Non-default thread affinity set probably by the OpenMP library, disabling internal thread affinity [proxy:0:0@leon304] HYDT_dmxu_poll_wait_for_event (./tools/demux/demux_poll.c:70): assert (!(pollfds[i].revents & ~POLLIN & ~POLLOUT & ~POLLHUP)) failed [proxy:0:0@leon304] main (./pm/pmiserv/pmip.c:387): demux engine error waiting for event [mpiexec@leon304] HYDT_bscu_wait_for_completion (./tools/bootstrap/utils/bscu_wait.c:101): one of the processes terminated badly; aborting [mpiexec@leon304] HYDT_bsci_wait_for_completion (./tools/bootstrap/src/bsci_wait.c:18): bootstrap device returned error waiting for completion [mpiexec@leon304] HYD_pmci_wait_for_completion (./pm/pmiserv/pmiserv_pmci.c:521): bootstrap server returned error waiting for completion [mpiexec@leon304] main (./ui/mpich/mpiexec.c:548): process manager error waiting for completion I tried to comment out the lower row involving [ intermolecular-interactions ] in the topology file and confirmed that the calculation was finished normally. (Of course, the ligand was leaving from the binding site when the ligand-receptor interaction are completely turned off.) Could you advice me how to solve this error?
You mean when you comment out all of the intermolecular interactions, or literally just the last line. If the latter, then you've found your problem.
-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.
