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
>
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Received on Wed Jul 21 2010 - 05:00:03 PDT
