On Thu, Feb 13, 2014 at 7:40 PM, satyanarayan rao <satyanar.usc.edu> wrote:
> Hi,
>
> I am new to amber md program.
> It would be a great help if some one can direct me where to find the
> charges for methylated cytosine atoms in latest version of amber force
> field ( or in earlier version).
>
A popular database of Amber charges and force field parameters is here:
http://www.pharmacy.manchester.ac.uk/bryce/amber/
They don't seem to have methylated cytosine, so you may have to use a tool
like R.E.D. (q4md-forcefieldtools.org) to derive charges for you (the
parameters are probably already available in the standard Amber force
fields).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Feb 14 2014 - 03:30:03 PST
