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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Received on Wed Feb 14 2007 - 06:07:48 PST
