Hi Aparna.P
You can use the "multi block" approach described in the RED.DB website
and in the tutorial [1,2] to obtain the RESP charges for your modified
nucleotides.
[1]
http://q4md-forcefieldtools.org/REDDB
[2]
http://q4md-forcefieldtools.org/Tutorial/
Stephane
Aparna P wrote:
> Sir,
> I am a research scholar working on simulation studies of nucleic acids
> ,their modifications and interactions with other molecules using AMBER
>
> We are trying to calculate partial atomic charges of modified nucleotides.
> In the case of base modification i read that we have to replace
> sugar-phosphate moiety by methyl group(charge compensating with
> sugar-phosphate moiety).
>
> But in the case of sugar modification when we calculate partial atomic
> charges by abinitio method, how can I account for the phosphate group(the
> bulky phosphate part is not working with abinitio calculation by Gaussian).
>
>
> It will be very helpful if you could make any suggestion for me.
>
>
>
>
> Aparna.P
>
> Research Scholar
>
> School Of Pure And Applied Physics
>
> M.G University
>
> Kottayam,Kerala,India
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Received on Fri Feb 11 2011 - 06:00:04 PST
