On Sat, Jan 21, 2012, Jio M wrote:
>
>
> 1) If I am studying two different ligands (one has polar atoms and
> other has more non-polar atoms) with same macromolecule (pocket being
> non-polar) in separate MD run having explicit solvent, Can I compare
> vdwaal energy directly from amber output file declaring contribution of
> vdwaal towards stability of complex? (less positive vdwaal energy more
> stable, less repulsion and more positive vdwaal less stable, means more
> repulsion)
If the two systems don't have exactly the same number of waters, then the
energy components cannot be compare. Even with the same number of waters,
looking at the total energy (or components of the total energy) is usually not
very helpful: they have very large fluctuations, and there is no reason to
suppose that there is any connection between complex stability and any of
these numbers.
The MM-PBSA type approach is better suited to trying to get an understanding
of the contributions to protein-ligand stabilities.
...good luck....dac
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Received on Thu Jan 26 2012 - 05:30:03 PST
