[AMBER] Hvdw: Non polar contribution to solvation in MMPBSA with solvent layer

From: Lekpa Duukori <duukori.gmail.com>
Date: Mon, 16 May 2011 11:43:02 -0600

Hi Everyone,

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?

Thanks for your time!

Lekpa.
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Received on Mon May 16 2011 - 11:00:02 PDT
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