AMBER Archive (2004)

Subject: Re: AMBER: About RESP Calculation

From: Qing Zhang (qingzhang_nyu_at_yahoo.com)
Date: Sat Mar 20 2004 - 00:43:03 CST

> > but as far as I understood, it is not possible
> because of the
> > orientation problem of the molecule at interest.
>
> The question is not "to be possible" or "not be
> possible to"... the question is
> the reproducibility of the published charges, that's
> it... F.

The published charges can be reproduced well, although
not exactly, if one strictly follows the paper:

Piotr Cieplak, Wendy D. Cornell, Christopher Bayly, &
Peter A. Kollman, "Application of the multimolecule
and multiconformational RESP methodology to
biopolymers: charge derivation for DNA, RNA, and
proteins", J. Comp. Chem., 16: 1357-1377, 1995.

Based on this paper and previous discussion with Dr.
Cieplak, I have formulated a protocol that produces
AMBER-compatible partial charges of
carcinogen-modified B-deoxynucleotides. The protocol
has been successfully applied to several
carcinogen-modified B-deoxynucleotides. One can also
easily apply it to other unusual deoxynucleotides. The
protocol is at:

http://monod.biomath.nyu.edu/~qzhang/BP-adenine/protocol.txt

The protocol includes how to modify a molecule
structure in insightII, how to optimize the structure
and produce ESP in Gaussian98, and how to produce RESP
charges in AMBER 6. The crystal structure should be
modified not only to reproduce AMBER partial charges,
but also to remove bumps between non-bonded atoms
because Gaussian does not know where the bonds are
given only atom coordinates. Optimization in Gaussian
(HF/6-31G*) can take several to ten days depending on
the molecule size and optimization convergence.

The protocol also comes with a few Perl programs that
make the procedure easy:

http://monod.biomath.nyu.edu/~qzhang/Research.htm

Hope this will help.

Sincerely,

Qing Zhang

=====

Ph.D. Candidate of Computational Biomolecular Chemistry

Department of Chemistry, New York University

   Phone: 917-509-3182 (cell) , 212-998-3593 (office)
   Email: qingzhang_nyu_at_yahoo.com , qz219_at_nyu.edu
   Homeage: http://www.qingzhang.net

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