Dear Satya,
just look at the web site Jason suggests:
http://www.pharmacy.manchester.ac.uk/bryce/amber/
If you click on "Nucleic acids" there, then the first parameter set you
see is for deoxy-5-methylcytosine (dmc), this may be what you want.
Good luck,
Filip
Jason Swails wrote:
> 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
>
>
--
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E-mail: filip.lankas.uochb.cas.cz
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Received on Thu Feb 20 2014 - 05:00:03 PST
