The Python version (MMPBSA.py) is a newer implementation of doing MM-PBSA
calculations for Amber simulations. The two programs will reproduce the same
binding energies given the same input values, despite the fact that they are
two different codes. There should be no problem with installing and running
MMPBSA.py on your cluster, except that you should be aware that the
decomposition analysis only works with Amber 11, as mentioned in the manual.
I hope that helps. Let us know if you have any other questions.
-Bill
On Wed, Mar 23, 2011 at 9:52 AM, Mahmoud Soliman <mahmoudelkot.gmail.com>wrote:
>
> Hi all,
> I am a new user to Amber and I am planning to do some MMPBSA binding
> energy
> for some enzyme-ligand complex. I went through the tutorial before I do
> that
> and I notice that the program uses Python scripts but on the cluster
> (Amber
> 10 installed) that I am going to run the calculation on I see that it is
> a
> Perl script pbsa.pl. I wonder is there any technical difference between
> pbsa.py and pbsa.pl I should be aware about before running the
> calculations?
> can I install the new version of MMPBSA on the cluster and still
> compatible
> with the Amber 10 version???
> Any help would be appreciated....
> Best wishes
> Mahmoud
>
> --
>
> *************************************************
>
> Mahmoud E. Soliman
>
> Computational Chemistry & Modeling (PhD)
>
> Department of Chemistry
>
> University of Bath
>
> Bath
>
> BA2 7AY
>
> United Kingdom
>
> [1]http://people.bath.ac.uk/mess20/
>
> [2]http://www.bath.ac.uk/person/812559
>
> References
>
> 1. http://people.bath.ac.uk/mess20/
> 2. http://www.bath.ac.uk/person/812559
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Wed Mar 23 2011 - 07:00:05 PDT
