From: David A Case <>
Date: Wed, 2 Jul 2014 07:55:18 -0400

On Wed, Jul 02, 2014, Zeinab Tavasoli wrote:
> I am performing free energy calculation with for a crystal
> structure of a protein-ligand complex.
> Although I have checked the structure of the complex after production and I
> am sure about the binding of ligand to its proper site, ΔG value is
> positive.

> I don't know where to look for the origin of this problem.

There could be many, many reasons for such a result. Errors can arise from a
poor force field, from lack of good equilibration, from the assumption of a
single trajectory model, or from the limitations of the implicit solvent
models used in the MM/PBSA model, or from problems with estimating
configurational entropies. Figuring this out is not something that is easily
"solved" on a mailing list--it is not even clear that there is a problem to be


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Received on Wed Jul 02 2014 - 05:00:03 PDT
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