thanks a lot sir 4 your valuable suggestion.
On Sat, Feb 12, 2011 at 12:55 AM, <cieplak.cgl.ucsf.edu> wrote:
> 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
> services/tools: http://q4md-forcefieldtools.org/RED/
>
> Best,
> Piotr
>
>
>
> > 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
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Received on Sun Feb 13 2011 - 23:00:02 PST
