I've noticed that the energy dropped significantly just before the job
terminated:
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.3342E+05 1.7748E+00 1.7075E+02 H9 4147
BOND = 10243.4116 ANGLE = 382.3810 DIHED =
4034.4069
VDWAALS = 25801.7886 EEL = -184077.5659 HBOND =
0.0000
1-4 VDW = 1142.8143 1-4 EEL = 9051.0550 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
50 -1.3425E+05 1.0214E+00 1.1301E+02 CD 2347
BOND = 10299.3244 ANGLE = 442.4051 DIHED =
4033.8846
VDWAALS = 25552.8101 EEL = -184186.6705 HBOND =
0.0000
1-4 VDW = 950.9742 1-4 EEL = 8652.4050 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
100 -3.1431E+05 1.1784E+06 1.8708E+08 H7 4100
BOND = 10489.7320 ANGLE = 828.3905 DIHED =
4105.2686
VDWAALS = 25580.9181 EEL = -184472.5186 HBOND =
0.0000
1-4 VDW = 778.4510 1-4 EEL = -171621.9397 RESTRAINT =
0.0000
On Mon, May 22, 2017 at 10:12 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> Noting that the stack indicates nonbonded adjustment as part of ewald
> force calculation (likely as not), have you looked for any warnings or
> odd energies in your output file prior to this event?
>
> Bill
>
>
> On 5/22/17 12:54 AM, Nikita Devnarain wrote:
> > Dear AMBER users
> >
> > I'm trying to minimise a complex with a receptor and 2 ligands, however,
> I
> > keep encountering the following error causing termination of the job:
> >
> > Program received signal SIGSEGV: Segmentation fault - invalid memory
> > reference.
> >
> > Backtrace for this error:
> > #0 0x2AAAAC453BF7
> > #1 0x2AAAAC452DF0
> > #2 0x2AAAAD10124F
> > #3 0x56C339 in nb_adjust_
> > #4 0x56E268 in ewald_force_
> > #5 0x7AAF93 in force_
> > #6 0x4E3712 in sander_
> > #7 0x4D93A6 in MAIN__ at multisander.F90:?
> >
> >
> > Could anyone assist me with what has been causing this?
> >
>
>
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>
--
Kind regards
Miss Nikita Devnarain
Pharmaceutical Chemistry (PhD)
Molecular Modeling and Drug Design Research Group
Discipline of Pharmaceutical Sciences
School of Health Science
University of KwaZulu-Natal
Westville Campus
Private Bag X54001
Durban 4000
South Africa
Website: http://soliman.ukzn.ac.za
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Received on Mon May 22 2017 - 01:30:03 PDT
