On Mon, 2014-03-24 at 08:31 +0500, loue chen 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.
I don't know what this means.
> Data for the comparison of MMGBSA and decomposition is attached along with
> mail. Please guide me to solve this problem.
What makes you say this is a problem? What you should look for is an
explanation for the trends you are seeing. It stands to reason that the
ligand experiences the largest difference in decomposed energy
contributions because almost all of its intermolecular interactions
occur between the ligand and protein atoms. In the unbound state, these
interactions disappear. Protein residues, on the other hand, maintain
the same interactions in both the bound and unbound states -- the only
contributions to the binding free energy occur from the interactions
between the protein and ligand.
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Mar 24 2014 - 05:00:02 PDT
