On 9/1/15 10:12 AM, Atsutoshi Okabe wrote:
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.
I understand what you want to do; I tested this code before it was merged so I
certainly know how it works :)
I'm seeking clarification on what you said before:
You said: "I tried to comment out the lower row involving [
intermolecular-interactions ] in the topology file and confirmed that the
calculation was finished normally."
What does this mean? The last line *only* or the entire
[intermolecular_interactions] directive? "Lower row" is not clear.
The simplest check is to make sure your global atom numbers are right; if they
aren't then the physics will of course be unsound.
-Justin
Bests,
Atsutoshi
2015/09/01 11:17、Justin Lemkul <jalem...@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@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
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==================================================
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
==================================================
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