Dear Colleagues
We are pleased to announce that the Antechamber module in the AMBER
package is now available as a separated package under the terms of the
GNU General Public License (GPL).
In molecular mechanics (MM) studies, atom types and/or bond types of
molecules are needed for energy calculations. We developed a set of
algorithms to perceive atom types and bond types automatically. The atom
types are defined in a description table that is independent of the
program itself. The bond types are determined just based on the atomic
connectivity of a molecule. The algorithms behind the manipulations may
be useful for other molecular mechanical packages as well as
applications that need to designate atom types and bond types.
Besides the atom type and bond type assignment, Antechamber can also be
used to perform molecular format conversions (like Babel); generate the
AM1-BCC, CM1, CM2 and Gasteiger charges; generate residue topology
files; search the missing force field parameters and provide reasonable
substitutes for a molecule. The combination of the Antechamber package
and the GAFF (General AMBER Force Field) makes it possible to model
protein-ligand interaction with the AMBER package automatically.
For more information on the antechamber package, please go to the
antechamber homepage:
http://amber.scripps.edu/antechamber/antechamber.html
Antechamber and GAFF citations:
1. Wang, J., Wang, W., Kollman P. A.; Case, D. A. "Automatic atom
type and bond type perception in molecular mechanical calculations"
Journal of Molecular Graphics and Modelling, 25, 2006, 247-260.
2. Wang, J., Wolf, R. M.; Caldwell, J. W.;Kollman, P. A.; Case, D.
A. "Development and testing of a general amber force field" Journal of
Computational Chemistry, 25, 2004, 1157-1174.
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Dr. Junmei Wang
Chemistry & Biophysics
Encysive Pharmaceuticals Inc.
7000 Fannin, Houston TX 77030
Tel: 713-578-6649
Email: jwang.encysive.com
http://amber.scripps.edu/antechamber/antechamber.html
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Received on Sun Feb 26 2006 - 06:10:19 PST
