AMBER Archive (2002)

Subject: Roar capabilities

From: M. L. Dodson (bdodson_at_scms.utmb.EDU)
Date: Fri Nov 08 2002 - 11:37:48 CST

A colleague asked me a question to which I don't know the answer, even
approximately, so I said I would pose it to the list.

There exists a certain class of N2-guanine adducts that form closed
6-membered rings between N2 (exocyclic) and N1 (endocyclic). It is
observed that the ring is closed in single stranded DNA, but the
N1-adduct bond is opened in double stranded DNA. The question they
asked is as follows:

Using the QM/MM coupled potential method in Roar, can one reasonably
estimate the equilibrium constant for the adducted DNA open<->closed
reaction when the DNA is bound to a protein (at the adduct site)?

Thanks.
Bud Dodson 

-- 
M. L. Dodson                                bdodson_at_scms.utmb.edu
409-772-2178                                FAX: 409-772-1790