AMBER Archive (2009)

Subject: [AMBER] Parametrizing charges for modified DNA bases

From: Bob Johnson (bobjohnson1981_at_gmail.com)
Date: Mon Dec 07 2009 - 12:05:09 CST

Hello everyone,
I would like to parametrize charges for DNA bases that contain some
chemical modifications. The modifications are pretty simple and
contain atom types that are already defined within the AMBER force
field.

In order to parametrize charges, however, I would like to follow the
method used for the rest of the DNA bases. That is, I would like to
fit the RESP charges to the bases while restraining the charges on the
sugar group to certain values. That way, this base should be
compatible with the rest of the bases in the AMBER force field. Is
there software that will aid in this process?

Thanks,
Bob 

-- 
Bob Johnson
Institute for Computational Molecular Science
Temple University
1900 North 12th Street
Philadelphia, PA 19122
http://astro.temple.edu/~rjohnson

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber