AMBER Archive (2009)

Subject: Re: [AMBER] mm-GBSA from implicit

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Sat Jan 10 2009 - 07:25:10 CST

yes, that is possible and has been reported in the literature.
see, for example,

Rizzo, R. C.; Toba, S.; Kuntz, I. D. A Molecular Basis for the
Selectivity of Thiadiazole Urea Inhibitors with Stromelysin-1 and
Gelatinase-A from Generalized Born Molecular Dynamics Simulations. J.
Med. Chem ., 2004, 47, 3065-3074.

On Fri, Jan 9, 2009 at 10:13 PM, Catein Catherine
<askamber23_at_hotmail.com> wrote:
>
> Dear Sir/Madam, I would like to do a mm-GBSA analysis. According to the tutorial, I should firstly do the explicit solvent simulation for the complex. Is it possible to do the simulation with implicit solvent, and extract the mdcrd files for mm-GBSA analysis? Best regards, CatSee all the ways you can stay connected to friends and family
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