AMBER Archive (2002)

Subject: counter-ions in FEP

From: Christophe L M J Verlinde (verlinde_at_u.washington.edu)
Date: Thu Jul 11 2002 - 11:37:41 CDT

I would like an opinion on the following FEP simulation:
My protein has a net charge of +3. In my simulations
with explicit TIP3P water I usually add counterions to
obtain a neutral system. However, now I am faced with
performing a FEP simulation in which a neutral ligand
is changed into an isosteric ligand with net charge -1.
Should I keep the system neutral in both states of the FEP?

Christophe L.M.J. Verlinde, Ph.D.
Associate Professor of Biochemistry
and Biological Structure

Biomolecular Structure Center
University of Washington - Box 357742
Health Sciences Building K-428A
1959 NE Pacific Ave
Seattle, WA 98195
T:(206)543-8865 F:(206)685-7002
URL: www.bmsc.washington.edu/people/verlinde