Dear Mathew,
What you can do with these structures is as follows: Remove the -PO2 part
and make them look like nucleosides (But start first from X-Ray
structures if there are any in the literature). You can optimize this
structure, and then do an ESP calculation to get the ESP data points.
Then, u can use 'resp' to get the RESP charges. You can then restrain the
sugar charges to the sugar charges of the DNA resiudues (This part is
tricky, beacause what u have is a nucleoside; not a nucleotide. The
easiest way is to combine the DX5 and DX3 residues to create the AMBER
nucleosides. You can, then, impose 'resp' program to assign these
sugar charges to your modified residues' sugar charges). This will create
the rest of the RESP charges for your modified residues.
Of course, this is not the resp protocole. This method assumes that the
RESP charges derived by Cornell et al. are right; and that you can use
these charges for any modified residues (meaning that the base and sugar
regions do not interact a lot). Good luck.
Best,
On Wed, 14 Feb 2007, mathew k varghese 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
>
> Mathew
>
> Raviprasad Aduri <rpaduri.chem.wayne.edu> wrote: Dear Mathew,
> I am not quite sure which modified nucleoside you are looking for. You can
> visit our website
> "http://ozone3.chem.wayne.edu:8080/Modifieds/" 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.
> Sincerely
> 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 mathew_kvarghese.yahoo.co.in
> >
> >===========================================================================
> >
> >
> >Here's a new way to find what you're looking for -
> >Yahoo!
> >Answers
>
>
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>
>
> /\/\athew
>
> Mathew K Varghese
> Research Scholar
> School of Pure and Applied Physics
> M.G.University
> Kottayam, Kerala
> India
>
> email mathew_kvarghese.yahoo.co.in
>
> ===========================================================================
>
> ---------------------------------
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--
Ilyas Yildirim
---------------------------------------------------------------
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Received on Wed Feb 14 2007 - 06:07:48 PST
