On Mon, 2014-03-24 at 09:28 +0530, Arunima Shilpi wrote:
> Dear Sir
>
> I followed the tutorial for MMGBSA and MMPBSA binding energy calculation.
> Here the binding energy for MMGBSA comes to be negative whule for MMPBSA
> comes to be positive.
>
> I request you to kindly guide me as to how to include the entropy papramter
> in the calculation of binding energy.
>
> While going through the mailing list I got the following option
>
> "To be comparable with the GB, you'll need to set inp=1, i.e. without
> the EDISPER".
>
> Here I dint get how to edit this parameter in mmpbsa.py file.
Did you look at the manual? On page 356 of the AmberTools manual it
lists the variables that belong in the &pb namelist, and inp is one of
them.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Mar 24 2014 - 05:30:03 PDT
