Re: AMBER: gibbs termination

From: David A. Case <>
Date: Wed, 14 Apr 2004 18:24:10 -0700

On Wed, Apr 14, 2004, Carsten Detering wrote:
> I am using Gibbs to determine deltadeltaG values for a ligand in a
> binding pocket.

(I'll make this my final comment, since my basic views were already stated
on this list on April 6.)

Gibbs is a very difficult program to use. Since you have to do the comparable
calculation for the free ligand anyway, my recommendation is that you do the
free ligand simulations first, since that should be faster, and it should be
easier to convince yourself that you understand what gibbs is doing. I would
also recommend that you equilibrate with gibbs, as getting sander7 or sander8
to work well with gibbs is quite tricky. (Principally, sander is designed to
do PME simulations, whereas gibbs is not.)


David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |
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Received on Thu Apr 15 2004 - 02:53:00 PDT
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