AMBER Archive (2004)

Subject: Re: AMBER: gibbs termination

From: David A. Case (case_at_scripps.edu)
Date: Wed Apr 14 2004 - 20:24:10 CDT

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.)

...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
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