AMBER Archive (2004)

Subject: AMBER: atom type CM

From: Kristina Furse (
Date: Fri Jan 16 2004 - 14:37:38 CST

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 E. Furse
Department of Chemistry
Center for Structural Biology
Vanderbilt University

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