On Fri, May 16, 2014 at 3:08 PM, loue chen <lauimi.883.gmail.com> wrote:
> *Dear Amber Experts,*
>
> I am running MD simulation for a protein ligand complex to determine
> selectivity. When I calculate the binding free energy, the MMGBS value is
> according to the published data. But when I perform energy decomposition
> using MMGBSA.py (Amber Tools 13) to calculate per residue contribution, all
> of the energy shift difference shifts toward ligand, and the contribution
> of amino acids become opposite.
>
Th
is is the exact same question you asked here:
http://archive.ambermd.org/201403/0406.html
(and I understand this no better now than I did then).
>
>
>
> I am using following input command for MMGBSA and decomposition. Please
> check it weather there is some problem in my input command or I am missing
> something. Or please if possible send me input command files for MMGBSA,
> and Decomposition. Mine are given below:
>
This part looks different, but still not helpful.
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri May 16 2014 - 21:30:03 PDT
