AMBER Archive (2007)

Subject: AMBER: RESP calculation of modified nucleotides

From: mathew k varghese (mathew_kvarghese_at_yahoo.co.in)
Date: Sat Feb 24 2007 - 00:50:23 CST

Dear Raviprsad and other amber users,

We have done the Gaussian calculations of the modified nucleotides by replacing the sugar and phosphate by methyl group. We got the ESP from the gaussian output and sucessfully produced the RESP inuts.

How can I costrain the methyl charges? Are we taking only the charges for the base atoms and using the charge values of sugar and phosphate from the normal nucleotides? The How can we costruct the parameters for the complete modified nucleotide to load into LEaP?

Thanks for the help

Mathew

/\/\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

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