[gmx-users] About the biotin parameter.....

[Justin Lemkul]

On 11/15/12 9:47 AM, rama david wrote:
> Hi Gromacs Friends,
>
>                      I want to do the simulation of system containing the
> biotin.
> I know that the charge calculated by prodrg is not good.
> I want to use the GROMOS96 53a6 force field  or OPLS force field.
> ( 1st choice is GROMOS second choice is OPLS)
>
> Please would you tell me how to get topologies for biotin with correct
> charge.
>

Most molecules in the Gromos force fields can be reasonably built from the 
charge group building blocks.  For biotin, the only trick is the thioether 
functional group, but perhaps there are parameters for that.  I know there has 
been a lot of recent work expanding the Gromos force fields, so someone may have 
done that already.

If suitable parameters aren't available, you need to read the primary literature 
for the parameter set you're using and derive parameters in a suitable way, 
which for Gromos would typically involve some preliminary QM calculations, free 
energy simulations, and empirical refinement.  The ATB server is also a 
possibility; it performs much better than PRODRG, but anything you get from an 
automated server should be validated first before being used in any simulation 
you care about.

-Justin
-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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