Could you post your MMPBSA.py input file was well as the corresponding
mdout files from both mmpbsa_py_energy and sander calculations? I would
guess that MMPBSA.py probably has one or two default values that are
different than the default values in sander, which would cause the slight
difference that you are seeing here.
-Bill
On Wed, May 9, 2012 at 7:01 PM, Damodaran, Komath <Komath.Damodaran.elan.com
> wrote:
> Hi,
>
> (I posted this question last week and didn't get any response. I am
> still wondering if anyone else has encountered this problem.)
>
>
>
> I ran a one step, energy calculation using the PB option using
> mmpbsa_py_energy and sander in Amber 11 on the same conformation of a
> protein-ligand complex.
>
>
>
> The mdin files were generated by the MMPBSA.py program using default
> parameters .
>
>
>
> The output matched for all except the EPB term which differed by about
> 30kcal/mol (-4452 vs -4489).
>
> I ran a similar test with the GB option on the same conformation. In
> this case the output matched for all except for the ESURF term, which
> differed by about 12kcal./mol
>
>
>
> The MMPBSA.py script in Amber11 uses mmpbsa_py_energy if no energy
> decomposition is requested. If decomposition is requested, it uses
> sander. So, for the same coordinates, if we run MMPBSA free energy
> calculations with and without decomposition, you get different results.
>
>
>
> Could anyone advise me what I am missing here?
>
>
>
> Thanks,
>
> Dam
>
>
>
>
>
>
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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 Fri May 11 2012 - 08:30:05 PDT
