Thanks professor. I will try it in serial and see…
The system is 226 amino acids in a cage of solvent. For doing it “by hand”, can you give me suggestions for where the procedure is explained?
Thanks again.
> On Nov 17, 2015, at 5:19 AM, David A Case <david.case.rutgers.edu> wrote:
>
> On Mon, Nov 16, 2015, Mohammad wrote:
>>
>> Thanks for your support. I looked at the output error (sorry I named the
>> job incorrectly that's why didn't see this in the beginning). It has
>> lots of errors that start with:
>>
>> /var/spool/torque/mom_priv/jobs/9489199.yak.local.SC: line 9: purge:
>> command not found
>> [n248:16483] 1 more process has sent help message help-mpi-runtime.txt /
>> mpi_init:warn-fork
>
> ...
>
> Do you know your jobs work in serial? Trying to run normal mode analysis with
> the parallel version of mm-pbsa can easily lead to lots of problems related to
> running out of memory. Plus, even if the problem is somewhere else, it is
> much harder to debug. (Apologies if you answered this question earlier.)
>
>> Line minimizer aborted: step at upper bound 0.0016720636
>
> How big is the system? If you are getting this sort of error, be sure to run
> single-frame NMA calculations, "by hand" if possible (i.e. don't use the
> mm-pbsa framework.)
>
> Jason will probably have more/better suggestions....
>
> ....dac
>
>
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Received on Wed Nov 18 2015 - 16:00:03 PST
