Hi,
I have found the problem described here :
http://archive.ambermd.org/201203/0332.html
I'm using AmberTools12 along with Amber11 installed as per the
instructions in the AmberTools 12 manual.
The problem appears with both the serial and parallel versions of
MMPBSA.py. I hit this problem when running per-residue free energy
decomposition on a one-trajectory set-up. Interestingly, I don't see the
problem when calculating the binding free energy of the system from a
three-trajectory set-up, even if I also require PB analysis.
I would like to know if this has been solved and there is a patch
available. I have applied all the 14 bugfixes for AmberTools 12, to no
avail.
Amber11 is patched up to patch 16, which I applied some time ago, before
installing AmberTools12. By the way I'm unsure how to apply further
patches to Amber11 now that I am using AmberTools12.
If a patch to solve this issue is not available, is the work-around
described in the above page safe to use?
Thank you!
--
Miguel
Architecture et Fonction des Macromolécules Biologiques (UMR7257)
CNRS, Aix-Marseille Université
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel: +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
mailto:miguel.ortiz-lombardia.afmb.univ-mrs.fr
http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia
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Received on Fri Jul 13 2012 - 05:30:04 PDT
