RE: AMBER: Modified nucleotides

From: Seth Lilavivat <>
Date: Mon, 12 Feb 2007 23:59:37 -0500

It depends on what you are using your modeling for. I use AM1-BCC for
my modified NA charges, but the goal of my modeling is to generate
reasonable structures. You should worry about where you are making the
largest error. An analogy would be if you were calculating the flow of
the Mississippi River it would make sense to worry if the average width
of the river was 500m or 500.5m.
-----Original Message-----
From: [] On Behalf
Of mathew k varghese
Sent: Monday, February 12, 2007 11:45 PM
Subject: AMBER: Modified nucleotides
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


Mathew K Varghese
Research Scholar
School of Pure and Applied Physics
Kottayam, Kerala



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Received on Wed Feb 14 2007 - 06:07:33 PST
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