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

[Atsutoshi Okabe]

Thanks, Justin.
I want to add restraint between protein and receptor using [intermolecular-interactions] section(not comment out [bonds], [angles] [dihedrals] lines)in new support tool of GROMACS 5.1.
But I got the error below and I don’t know what causes the problem.

Bests,
Atsutoshi

2015/09/01 11:17、Justin Lemkul <jalemkul at vt.edu> のメール：

> 
> 
> 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
> 
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