Re: [AMBER] parametrization of sugar modified nucleic acids

From: <>
Date: Fri, 11 Feb 2011 11:25:19 -0800 (PST)

For developing charges for any type of nucleotides we run qm calculations
for base+sugar moiety then for di-methyl-phosphate to obtain electrostatic
potentials. And then we use RESP program to "sew" those two or more
molecules together using additional charge constraints, charge
equivalencing etc. (See: Cieplak et al. J.Comput.Chem. 16,1357-1377 (1995))
However, different scenarios for developing of electrostatic potentials
by fitting together several molecules can be thought of, as well, (which
we are exploring now).
The entire process of charge fitting could be faciliated by R.E.D. web


> 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 - 11:30:05 PST
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