[AMBER] mm_pbsa.pl in PARALLEL does not finish

From: Anselm Horn <Anselm.Horn.biochem.uni-erlangen.de>
Date: Mon, 12 Jul 2010 18:55:32 +0200

Dear all,

I'm running an Nmode-Analysis of MM-PBSA from Amber11 (no patches) for a
ligand-receptor-complex in parallel using the mm_pbsa.pl script. The
input variable PARALLEL is set to 16, the number of cores on the local

However, the script does not finish properly:
After analyzing the last computed snapshot of the complex (entry in the
log file: "Ana entropy"), it does not proceed to compute the receptor or
the ligand coordinate files. The computing machine still has 16
mm_pbsa.pl processes running with 100%, but nothing happens, no further
output is generated until the queuing system kills the job.

I then tried the case with just the receptor marked for analysis in the
mm_pbsa.in file, but the same thing occurred: After computing all
entropy contributions for the receptor snapshots the script hangs before
doing the final statistics analysis and output. The last file generated
is the <file>_rec.all.out.

It seems to me that the child processes do not finish properly, but
maybe I also have an error in some input settings?
Has anybody experienced a similar behaviour - and found a remedy?

I'm looking forward to your hints, because I very much appreciate the
fact that mm_pbsa.pl has been made parallel.


Anselm Horn

Institut für Biochemie
Friedrich-Alexander-Universität Erlangen-Nürnberg

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Received on Mon Jul 12 2010 - 10:00:07 PDT
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