AMBER Archive (2006)

Subject: Re: AMBER: Which one is the best force field for DNA?

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Thu Apr 13 2006 - 03:11:33 CDT

Dear Chengwen,

I used ff99 for RNA .... And I believe we should aim at using one force
field for both nucleic acids and proteins for the simple reason that in
nature they coexist and cannot function one without the other .... Also,
my understanding of the Amber ffs is that a newer version does retain
the attributes of an older version (unless proven faulty) so ff99 should
retain the torsion angle parameters involving the glycosidic torsion
from ff98. From my experience ff99 should be OK ... However I dont have
experience with the polarizable ffs....

Best wishes
vlad

Chengwen Chen wrote:

> Dear all,
>
> I am modeling the 12-bps B-DNA with platinum bound to it. I wonder is
> parm98 the best force field for carrying out MD simulation with
> SANDER in AMBER 8? Or parm99 is better?
> I learned form AMBER 8 manual that ff98 is for nucleic acid and ff99
> "points toward a common force field for proteins for 'general' organic
> and bioorganic systems". So ff98 is better ? But the AMBER Tutorial of
> modeling DNA use the ff99. So I am confused.
>
> Thank you for your kindly reply.
>
>
> Best Wishes,
> Wendy 

-- 
Dr. Vlad Cojocaru
EML Research gGmbH
Molecular and Cellular Modeling Group
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg, Germany
Phone: +49-6221-533266
Fax: +49-6221-533298
e-mail: Vlad.Cojocaru_at_eml-r.villa-bosch.de
http://projects.villa-bosch.de/mcm/people/cojocaru/

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