On Tue, Jan 22, 2013, colvin wrote:
>
> I use mmpbsa.py to calculate the free energy binding using a set of
> 120 snapshots and the Delta total = -14.5391 (using GB, no entropy).
>
> Later on, i turn on entropy=1 on the same system, and the result
> showed that: Using Quasi-Harmonic entropy approximation: Delta G
> binding = 32.7203 (Delta S total = -47.2595).
>
You should indeed expect big changes in the binding free energy due to entropy
loss of the ligand upon binding. There are tons of articles on this: try a
Google search on "ligand entropy loss upon binding". I'm also partial to a
paper I wrote, that explains some of the difficulties in using the
quasiharmonic approximation for entropies:
.Article{Gohlke04a,
author = {Gohlke, H. and Case, D.A.},
title = {{Converging Free Energy Estimates: MM-PB(GB)SA Studies on the
Protein-Protein Complex Ras-Raf}},
journal = {J. Comput. Chem.},
volume = {25},
pages = {238-250},
year = {2004}
}
...dac
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Received on Tue Jan 22 2013 - 05:00:03 PST
