AMBER Archive (2004)

Subject: Re: AMBER: atom type CM

From: Junmei Wang (JWang_at_encysive.com)
Date: Fri Jan 16 2004 - 15:13:19 CST

When we developed parm99 modeling some small molecules, Prof. Kollman
suggested us to apply 'CM' for non-conjugated sp2 carbon in alkenes. This
is the reason that there are some parameters with "Junmei et al, 1999" in
the comments. Therefore, you may assign the non-conjugated sp2 carbon in
alkenes to "CM" if you use parm99.

Best

Junmei

===============================================================
Dr. Junmei Wang
Chemistry & Biophysics
Encysive Pharmaceuticals
7000 Fannin, Houston TX 77030
Tel: 713-5786649
Email: jwang_at_tbc.com
Homepage: http://sigyn.compchem.ucsf.edu/members/jmwang/index.html
===============================================================

                                                                           
             Kristina Furse
             <kristina.e.furse
             @vanderbilt.edu> To
             Sent by: amber <amber_at_scripps.edu>
             owner-amber_at_scrip cc
             ps.edu
                                                                   Subject
                                       AMBER: atom type CM
             01/16/2004 02:37
             PM
                                                                           
                                                                           
             Please respond to
             amber_at_scripps.edu
                                                                           
                                                                           

Hello all-

I'm curious about atom type CM. It is defined as "sp2 C pyrimidines in
pos. 5
& 6" in parm99.dat, but seems to have many parameters that don't apply to
standard nucleic acids. I've heard that there used to be an atom type for
isolated (non-conjugated) double bonds. Is that CM? If so, would CM still
be
appropriate for isolated double bonds or have the parameters been altered
in
order to better suit pyrimidines?

I see that many of the CM parameters have Junmei et al, 1999 in the
comments.
Does this refer to a specific paper? I haven't been able to find one from
1999
with Junmei Wang in the author list that seems to fit the bill. Am I
overlooking something painfully obvious?

Thanks for any insight!
Kristina

****************************************************
Kristina E. Furse
Department of Chemistry
Center for Structural Biology
Vanderbilt University
email: kfurse_at_structbio.vanderbilt.edu

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