On Mon, May 23, 2011, Lekpa Duukori wrote:
>
> I have a question about Hvdw (as reported in Gohlke and Case, JCC, 2004,
> 25(2), p238). They used a 15A spherical solvent layer in computing this
> parameter. What I want to know is the mechanics of doing this with
> AMBER/ptraj. I am doing double trajectory MMGBSA and I have to do it by hand
> (that is not using MMPBSA.py or pl). The VDWAALS energy in mdout files
> contains both solute-solvent and solvent-solvent interactions. My question
> is, do I do a single point on each solute+solvent snap shot, remove the
> solute then do another single point and take the difference between these
> numbers?
I think we used a special program back then, but what you describe sounds like
a reasonable approach. You may(?) need a third snapshot, with solute alone,
to get a complete division: solute-solute, solvent-solvent, and
solvent-solute.
...good luck...dac
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Received on Tue May 24 2011 - 09:00:02 PDT
