AMBER Archive (2007)

Subject: Re: AMBER: Modified nucleotides

From: Thomas Cheatham (tec3_at_utah.edu)
Date: Mon Feb 12 2007 - 23:03:38 CST

> 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?

It is not clear, but I would expect it to be OK. However, you might as
well take advantage of the resource of the Santalucia group if you can, see:

http://structbio.vanderbilt.edu/archives/amber-archive/2006/3103.php

or

http://ozone3.chem.wayne.edu:8080/Modifieds/

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