Re: AMBER: How to add water to calculate MMPBSA. .

From: <>
Date: Thu, 15 Dec 2005 11:13:30 -0600

>>>>> "David" == David A Case <> writes:

    David> The whole point of MM/PBSA is to treat the solvent as a
    David> continuum. So, including water molecules would lead to
    David> some other type of theory, which would have to be developed
    David> and tested. I am not aware of anyone who has done this.

Well, Dilip and I did something just a little like this for water near
an ion in a channel. We found that including the first solvation
shell explicitly (at the TIP3P level) give improved agreement with
all-atom thermo methods for channel--bulk Delta G. [Asthagiri and
Bashford, Biophys. J. 82:1176 (2002)].

It would be a project in itself to try out such ideas for the sort of
binding problems for which MM/PBSA is typically used though.


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Received on Thu Dec 15 2005 - 17:53:00 PST
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