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Symmetrization of the AMBER and CHARMM force fields

✍ Scribed by Edyta Małolepsza; Birgit Strodel; Mey Khalili; Semen Trygubenko; Szilard N. Fejer; David J. Wales

Publisher
John Wiley and Sons
Year
2010
Tongue
English
Weight
380 KB
Volume
31
Category
Article
ISSN
0192-8651

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✦ Synopsis

Abstract

The AMBER and CHARMM force fields are analyzed from the viewpoint of the permutational symmetry of the potential for feasible exchanges of identical atoms and chemical groups in amino and nucleic acids. In each case, we propose schemes for symmetrizing the potentials, which greatly facilitate the bookkeeping associated with constructing kinetic transition networks via geometry optimization. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010

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