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: case_at_scripps.edu
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 | http://www.scripps.edu/case
==================================================================
Received on Wed Aug 14 2002 - 08:33:57 PDT
