Thanks Dave. I am thinking I will need to use an infinite cutoff (say
cut=999) in these single points.
Emmanuel.
On Tue, May 24, 2011 at 9:52 AM, David A. Case <case.biomaps.rutgers.edu>wrote:
> 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 - 17:30:03 PDT
