AMBER Archive (2002)

Subject: Re: GB in Amber7

From: David A. Case (case_at_scripps.edu)
Date: Wed Aug 14 2002 - 10:33:57 CDT

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 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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