Subject: CCL: Re: need literature help on MD simulation of AdoMet

From: Eric Bennett <ericb<<at>>POBOX.COM>
Date: Sat, 19 Mar 2005 10:43:54 -0600

jz7<<at>>duke.edu wrote:

>Dear all,
>
>I want to run a MD on a protein which has AdoMet as a cofactor. But
>currenctly there is no parameter for the cofactor AdoMet in Amber or
>Charmm.
>
>  
>
Another paper which might get you started is:

George D. Markham, Per-Ola Norrby, and Charles W. Bock
S-Adenosylmethionine Conformations in Solution and in Protein Complexes: 
Conformational Influences of the Sulfonium Group
Biochemistry 2002, 41, 7636-7646

However, these parameters were determined for the old Amber 3 force 
field and they were used only for conformational energy comparisons, not 
for dynamics.

-- 
Eric Bennett, Center for Drug Design, U of Minnesota

Drawing on my fine command of the language, I said nothing.
-Robert Benchley