If you really want to use OPLS/AA then you can find DNA parameters on the
Gromacs website using the following link.
http://www.gromacs.org/component/option,com_docman/task,doc_details/gid,45/Itemid,26/
However i am not sure that these parameters are well tested and i am not
sure if they have been used in many/any published works. Like Justin said
the AMBER forcefields would be a better option unless you need OPLS/AA for
a specific reason, for more info on the AMBER forcefields in Gromacs see:
http://chemistry.csulb.edu/ffamber/
Hope this helps
Tom
--On Tuesday, September 02, 2008 21:24:45 -0400 "Justin A. Lemkul"
<[EMAIL PROTECTED]> wrote:
Jeff Woodford wrote:
Hi all,
Forgive me if this is a stupid question, but:
I am attempting to simulate the interaction between a peptide and a DNA
strand using the OPLS/AA force field. However the parameters for the
DNA bases don't appear to be included. Where might I find these
parameters suitable for adapting to GROMACS?
Any particular motivation for using OPLS-AA? The AMBER force fields
include both DNA and protein.
-Justin
Thanks in advance,
-Jeff
Jeffrey N. Woodford
Associate Professor of Chemistry
Eastern Oregon University
Tel: 541-962-3321
Fax: 541-962-3873
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========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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TJ Piggot
[EMAIL PROTECTED]
University of Bristol, UK.
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