AMBER Archive (2002)

Subject: Including explicit waters in GB dynamics

From: Kristina Furse (kristina.e.furse_at_vanderbilt.edu)
Date: Sat Jul 20 2002 - 19:30:43 CDT

Hello-

I am running some dynamics on a crystal structure using generalized Born to
approximate solvent, but would like to include a few explicit crystallographic
water molecules that are somewhat buried and appear to be interacting with the
protein in interesting ways. I was wondering if AMBER GB is calibrated for
this type of hybrid continuum/explicit water calculations? Any advice?

Thanks for any response!

Kristina

****************************************************
Kristina E. Furse
Department of Chemistry
Center for Structural Biology
Vanderbilt University
email: kfurse_at_structbio.vanderbilt.edu