[gmx-users] Parameters for DNA bases

[TJ Piggot]

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" 
<jalemkul at vt.edu> 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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>>
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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
t.piggot at bristol.ac.uk
University of Bristol, UK.