[AMBER] parametrization of sugar modified nucleic acids

From: Aparna P <aparnaspap.gmail.com>
Date: Fri, 11 Feb 2011 15:16:13 +0530

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.


Research Scholar

School Of Pure And Applied Physics

M.G University

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Received on Fri Feb 11 2011 - 02:00:04 PST
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