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

From: Thomas Cheatham <>
Date: Thu, 15 Dec 2005 11:09:47 -0700 (Mountain Standard Time)

> 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)].

We (Spackova, Sponer, Cheatham et al) investigated this issue with DNA
minor groove binding drugs; it is discussed in the main text and
supplementary material. JACS 125, 1759 (2003).

\-/ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy
-/- Departments of Med. Chem. and of Pharmaceutics and Pharm. Chem.
/-\ Adjunct Asst Prof of Bioeng.; Center for High Performance Computing
\-/ University of Utah, 30 S 2000 E, SH 201, Salt Lake City, UT 84112
/-\ (801) 587-9652; FAX: (801) 585-9119
\-/ BPRP295A

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Received on Thu Dec 15 2005 - 18:53:01 PST
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