I'll try that...thanks for the help!
On Mon, May 22, 2017 at 10:27 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> Dropping significantly is normal. I suggest printing every step, to see
> what happens right at the end.
>
> One of my favorite hacks for all situations is to run a little md at 10K
> instead of minimization, then minimize if you must. If your coordinates
> are the problem, it might bump you out of the situation. I say this
> since min ran a bit, indicating no basic problem with the model, so the
> coordinates are suspect.
>
> Bill
>
>
> On 5/22/17 1:19 AM, Nikita Devnarain wrote:
> > 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?
> >>>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon May 22 2017 - 02:00:02 PDT
