AMBER Archive (2007)

Subject: Re: AMBER: Modified nucleotides

From: Raviprasad Aduri (rpaduri_at_chem.wayne.edu)
Date: Tue Feb 13 2007 - 11:23:15 CST

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_at_yahoo.co.in
>
>===========================================================================
>
>
>Here's a new way to find what you're looking for -
><http://us.rd.yahoo.com/mail/in/yanswers/*http://in.answers.yahoo.com/>Yahoo!
>Answers

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