[gmx-users] Parameters for DNA bases

[Justin A. Lemkul]

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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-- 
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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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