Just as clarification, MMPBSA.py should work just fine with Amber 9
(excluding decomposition calculations which only work properly with Amber
11), as long as all bug fixes have been applied to Amber and you are using
the most recent release of AmberTools (AmberTools 1.4).
Good luck!
-Bill
On Wed, Jul 21, 2010 at 7:32 AM, Asfa Ali <asfa.iisc.gmail.com> wrote:
> Hi,
>
> Actually we have the licenced version of Amber9 and mmpbsa.py is not
> applicable there. I tried to run mm_pbsa.pl in desktop pc but it is
> running
> for a very very long time making the computer very slow.
>
> So I wanted to run it in a cluster but I don't have the script to run it
> parallelly..
>
>
> On Wed, Jul 21, 2010 at 4:51 PM, Anselm Horn <
> Anselm.Horn.biochem.uni-erlangen.de> wrote:
>
> > Hello Asfa,
> >
> > > Is it possible to run mm_pbsa.pl in parallel? If so, can u plz give
> the
> > > procedure and script for parallel-mmpbsa.
> > it's described in the Amber11 manual.
> > You just have to set PARALLEL to 1 (see also
> > $AMBERHOME/src/mm_pbsa/Examples/10_MMPBSA_Binding_Parallel/mm_pbsa.in).
> >
> > However, I have not been able to complete a parallel mm_pbsa.pl run
> > sucessfully (cf my previous e-mails).
> >
> > Jason wrote, that the python version MMPBSA.py had a working MPI
> > parallelization implemented. So maybe you should try this out.
> >
> > Regards,
> >
> > Anselm
> >
> > Bioinformatik
> > Friedrich-Alexander-Universität Erlangen-Nürnberg
> > Germany
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Wed Jul 21 2010 - 05:00:04 PDT
