Re: AMBER: Modified nucleotides

From: Raviprasad Aduri <>
Date: Wed, 14 Feb 2007 19:58:39 -0500

Dear Mathew,

I went through your pdb files and would like to suggest the following.

If you are planning to do the RESP charge fitting (which may take some time
for you to figure out), what you can do is as follows.
You can remove the sugar part (including the phosphate) and attach a methyl
group in place of the sugar and then do the GAUSSIAN
calculations on the methylated base alone. I suppose that you want to use
these parameters in AMBER, in which case you want to be consistent with the
AMBER original procedure, for which you need to compute the ESP using
Mertz-Kollman procedure (the keyword 'pop=mk' in GAUSSIAN) and also the
geometry optimization needs to be done at HF theory using 6-31G(d) basis
set. Once you have the ESP computed, then you can do RESP to obtain the
modified base charges. This is done in a two stage manner and examples of
which are available in the AMBER manual. To constrain the methyl group
(that replaced the sugar), you can either use the overall charge of
2'deoxyribose sugar from AMBER or use 0.092541e (the value from our
studies on DNA).

Can you give me some information about where these modifications are found
(are they naturally occurring or artificially synthesized).

I hope this will give you a starting point to think about and wish you all
the best.

Raviprasad Aduri

At 10:47 PM 2/13/2007, you wrote:
>Dear Raviprasad,
>I have already visited your site, (from the link in AMBER site).
>I am trying to do the simulation of a DNA molecule (NMR structure). Some
>of the bases contains an extra ring. We have tried to do a Gaussian
>calculation but I could not get the ESP charges from the output. That is
>why I am asking the question.
>The pdb files of the molecules are attached.
>Would you please direct me how to do the charge calculation?
>Thanks in advance
>Raviprasad Aduri <> wrote:
>Dear Mathew,
>I am not quite sure which modified nucleoside you are looking for. You can
>visit our website
>"" and download the parameters
>for the modification you are interested in.
>If you do not find the modification you are interested on our website,
>please mention the modification you are interested in and we might have
>done the calculations on that and
>I can send you the parameters.
>Raviprasad Aduri
>At 11:44 PM 2/12/2007, you wrote:
> >Dear AMBER users,
> >
> >
> >I am planning to do some MD simulations of modified nucleic acids. Is it
> >reasonable to use the am1-bcc charges for the modified nucleotides?
> >
> >Thanks in advance
> >
> >
> >Mathew K Varghese
> >
> >
> >
> >/\/\athew
> >
> >Mathew K Varghese
> >Research Scholar
> >School of Pure and Applied Physics
> >M.G.University
> >Kottayam, Kerala
> >India
> >
> >email
> >
> >===========================================================================
> >
> >
> >Here's a new way to find what you're looking for -
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>Mathew K Varghese
>Research Scholar
>School of Pure and Applied Physics
>Kottayam, Kerala
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Received on Sun Feb 18 2007 - 06:07:13 PST
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