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.tbc.com
Homepage: Http://sigyn.compchem.ucsf.edu/members/jmwang/index.html
===============================================================
Kristina Furse
<kristina.e.furse
.vanderbilt.edu> To
Sent by: amber <amber.scripps.edu>
owner-amber.scrip cc
ps.edu
Subject
AMBER: atom type CM
01/16/2004 02:37
PM
Please respond to
amber.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.structbio.vanderbilt.edu
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Received on Sun Jan 18 2004 - 19:53:06 PST
