[AMBER] MMGBSA doesn't finish

From: Bernhard Poll <poll.chemie.uni-hamburg.de>
Date: Fri, 24 Oct 2014 08:22:40 +0200

Hi everybody,

I've got some issue with MMGBSA-calculation with Amber11. I'm
calculating the energies for a larger dataset which works fine for a
bunch of ligands but and some but at some point (which seems to be
pretty random) the calculation doesn't finish which means it does write
the all temporary files (_MMGBSA_gb_ligand.mdout etc. ) and at the end
of each file it says "MM/GBSA processing done" but doesn't write the
Results.dat-file. Interestingly if I re-ran the calculation it finished
so there's no issue with the inputfiles I guess. I also double-checked
the input files and the md-simulations by visualisation, acdoctor etc.
and everything looks fine too. Maybe its some installation-issue but
then it won't work at all?!We switched also from openmpi to mpd for
parallelisation maybe that's an issue? Maybe some of you have an idea.

Thanks in advance.



Bernhard Poll
Institut für Pharmazie
Bundesstr. 45
D 20146 Hamburg | Raum 112
Tel:   +49 (0)40 42838-3626
mail: poll.chemie.uni-hamburg.de
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Received on Thu Oct 23 2014 - 23:30:02 PDT
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