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? Thank you, Atsutoshi Okabe -- 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.
