Re: [AMBER] error with NMA calculation

From: David A Case <>
Date: Tue, 17 Nov 2015 07:19:03 -0500

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....


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Received on Tue Nov 17 2015 - 04:30:03 PST
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