[gmx-users] Free energy calculation using inter-molecular bonded interaction

[Justin Lemkul]

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 at leon304] HYDT_dmxu_poll_wait_for_event (./tools/demux/demux_poll.c:70): assert (!(pollfds[i].revents & ~POLLIN & ~POLLOUT & ~POLLHUP)) failed
> [proxy:0:0 at leon304] main (./pm/pmiserv/pmip.c:387): demux engine error waiting for event
> [mpiexec at leon304] HYDT_bscu_wait_for_completion (./tools/bootstrap/utils/bscu_wait.c:101): one of the processes terminated badly; aborting
> [mpiexec at leon304] HYDT_bsci_wait_for_completion (./tools/bootstrap/src/bsci_wait.c:18): bootstrap device returned error waiting for completion
> [mpiexec at leon304] HYD_pmci_wait_for_completion (./pm/pmiserv/pmiserv_pmci.c:521): bootstrap server returned error waiting for completion
> [mpiexec at 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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================