[AMBER] STOP no longer optional in mm_pbsa.pl

From: <Don.Bashford.stjude.org>
Date: Tue, 16 Nov 2010 06:01:28 -0600

STOP is said to be an optional parameter in the mm_pbsa.in file, but I
find that if I follow my old practice of letting it take the default
(very large) value and count on the non-existence of the crd files to
exit the loop over snaphots, I get an indefinite hang. It goes
successfully through all the _com calculations but then never
continues on to the _rec or _lig. I think the problem is that the

  last if(! -e $ncrdfile);

at line 173 in mm_pbsa_calceneent.pm causes an exit from the loop in
between calls of the start and finish routines of the ForkManager, so
then the subsequent wait_all_children waits forever for the finish of
the last child.

If I set STOP to the correct value (or a value for which a crd still
exists) then all is well.


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Received on Tue Nov 16 2010 - 04:30:02 PST
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