Re: GB in Amber7

From: David A. Case <>
Date: Wed 14 Aug 2002 08:33:57 -0700

On Wed, Aug 14, 2002, Jithesh wrote:
> I'm planning to do simulation of a protein-DNA complex using the continuum
> solvent model. Which of the four methods available in Amber7 (igb) will be
> the best for this GB calculaton?

The igb=1 is the only one that has been tested very extensively, and would
be recommended for general use. igb=2 is something we are working on, but
the main paper describing its advantages and disadvantages has not yet been
published. igb=3 or 4 are primarily intended for analysis of snapshots taken
from other simulations, and not for MD simulations.

A good reference for Amber-specific aspects of GB is:

%A V. Tsui
%A D.A. Case
%T Theory and applications of the generalized Born solvation model in
macromolecular simulations
%J Biopolymers (Nucl. Acid. Sci.)
%V 56
%P 275-291
%D 2001

..good luck...dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
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Received on Wed Aug 14 2002 - 08:33:57 PDT
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