What do you mean "only on a selection of residues"? All MM/PBSA scripts (
mm_pbsa.pl and MMPBSA.py) do is prepare input files and call sander.
MMPBSA.py does not automatically set up calculations to only calculate
energy contributions to only a selection of residues. However, you can use
the "decomposition" option to print out energy contributions for each
(selected) residue. It won't save time computationally, since the force()
routine is executed for every atom. It is detailed in the manual. The
entropy is not decomposable with MMPBSA.py.
Hope this helps,
Jason
On Tue, Oct 5, 2010 at 11:01 AM, Federica Chiappori <
federica.chiappori.itb.cnr.it> wrote:
> Dear Amber users,
> I am calculating entropy and enthalpy of a protein-protein complex, with
> mmpbsa.py (AMBER11). Is it possible to run this program only on a
> selection of residues?
>
> Thanks
> Federica
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Tue Oct 05 2010 - 08:30:05 PDT
