Symmetrization of the AMBER and CHARMM force fields

J Comput Chem. 2010 May;31(7):1402-9. doi: 10.1002/jcc.21425.


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.