Mathew,
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.
Seth
-----Original Message-----
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf
Of mathew k varghese
Sent: Monday, February 12, 2007 11:45 PM
To: amber.scripps.edu
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
/\/\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!
<
http://us.rd.yahoo.com/mail/in/yanswers/*http:/in.answers.yahoo.com/>
Answers
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Feb 14 2007 - 06:07:33 PST
