AMBER Archive (2004)

Subject: AMBER: Glycam04

From: Karl N. Kirschner (crux5_11_at_yahoo.com)
Date: Wed Mar 24 2004 - 13:37:56 CST

Hi everyone,
  The new version of the Glycam parameter file set for
carbohydrate modeling is available on the AMBER8
distribution and at our web site
(http://glycam.ccrc.uga.edu).
  There are two sets of parameters: one without extra
points (aka electron lone pairs), and one with extra
points. These files include a leaprc (leaprc.Glycam),
carbohydrate prep files with ensemble average charge
set (Glycam04.prep), and the parameter file
(Glycam04.dat). The files associated with extra
points have "EP" in the file name.
  At all times, our website will contain the most
recent version of the Glycam parameter file set. Over
time, we will be adding additional prep residues and
modify the other files as the need arises.
  Please feel free to comment about this parameter set
and make suggestions about how it may be improved in
the future. Also, please comment on any bugs that you
might find when using these files. As pointed out
before, please read the AMBER8 manual before
implementing Glycam04.

Happy modeling,
Karl

=====
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Karl Nicholas Kirschner, Ph.D.
National Institute of Health Fellow
Complex Carbohydrate Research Center
University of Georgia - Athens, Ga USA
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