Symmetrization of the AMBER and CHARMM force fields

TitleSymmetrization of the AMBER and CHARMM force fields
Publication TypeJournal Article
Year of Publication2010
AuthorsMalolepsza E, Strodel B, Khalili M, Trygubenko S, Fejer SN, Wales DJ
JournalJournal of Computational Chemistry
Volume31
Pagination1402-1409
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.