AMBER Archive (2009)
Subject: Re: [AMBER] Parallel sander & polarisability
From: case (case_at_biomaps.rutgers.edu)
Date: Thu Oct 29 2009 - 12:02:28 CDT
On Thu, Oct 29, 2009, Thomas Taylor wrote:
> PMEMD clearly does not support polarisation (stated on p.200 in the Amber 10
> manual) - unless using the amoeba forcefield, which I do not. Sander on the
> other hand does, but the parallel version seems not to work so well, it
> crashes with an internal fortran error, having trouble converting something
> from the prmtop file.
> My Amber (and all mentioned versions of sander and chamber) is actually some
> approx. 1 month old checkout of the amber11 cvs. The prmtop files are generated
> via chamber (which I costumised to translate polarisabilities).
Well, the obvious question: do the test cases pass? Especially the
dna_pol and ubiquitin ones? This will help distinguish between types of
If you are taking chamber prmtops and customizing them, you are probably
venturing into unexplored territory here. Given that neither amber11 nor
chamber have been released yet, you should direct followups to the
amber-developers mailing list.
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