On Fri, 2014-02-28 at 05:49 +0000, de Waal, Parker wrote:
> On followup: I also ran a GB calculation and the delta G total seems
> more reasonable ->
> https://gist.github.com/anonymous/7f039c17c85d82cb880f
If you look at the results closely, you'll notice that the main
difference between the GB and PB results come from the nonpolar
solvation free energy. In GB, this value (ESURF) is -5.7320 in the
"Differences" section. In PB, this value (ENPOLAR+EDISPER) is +29.4216.
The polar solvation energy is far closer (EGB = 20, EPB = 34).
Therefore, almost the entire difference between these two values derives
from the difference in the nonpolar solvation model employed by each
approach.
You can set "inp=1" in the &pb section to use a simple surface
area-based model (you should recompile Amber to make sure you have all
available updates). The current default in AmberTools 13 MMPBSA.py is
inp=2 which uses a two-component model comprised of a repulsive
cavitation term offset by an attractive dispersion term.
Ultimately MM/PBSA does a poor job predicting absolute binding free
energies, though, and is useful mainly for rank-ordering different
ligands with a target (or different mutant targets with the same
ligand).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Feb 28 2014 - 05:00:03 PST
