Re: [AMBER] mm_pbsa.pl in PARALLEL - part 3

From: Jason Swails <jason.swails.gmail.com>
Date: Wed, 21 Jul 2010 10:59:52 -0400

Hello,

As Bill said, MMPBSA.py can be used with amber9, you just have to apply the bug fixes to both amber and mmpbsa. To get entropy to work, you have to use ambertools1.4. You may also have to edit the pb input file for pb calculations, I can't remember. You can also get the parallel version working for the python script.

The perl script can be run in parallel by using the variable PARALLEL #, where # is the number of processors. This is only available in amber11, though.

Hope this helps,
Jason

--
Jason Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
On 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
>> 
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>> 
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Received on Wed Jul 21 2010 - 08:30:03 PDT