Subject: AMBER opt for anions of stacked NAB's

From: Dayle Smith <[email-masked]>
Date: Thu, 20 Apr 2000 10:21:52 -0700 (MST)

CCL subscribers:

Can I use the Amber molecular mechanics method with the 1995 Cornell force
field to optimize the geometries of anions of stacked DNA bases (A,T,G,C)? 
I'm sure that the method works well for stacked neutral dimers, but I'm
not certain that anions of bases can be well described.

Thank you.

-Dayle Smith
[email-masked]
Ph.D. student
University of Arizona
Department of Chemistry