Internal coordinate modeling of DNA: Force field comparisons

The Jumna internal coordinate program for modeling nucleic acids was extended to include the force field developed for the Amber program. This forms a bridge between internal and Cartesian coordinate modeling approaches. Using the extensive conformational mapping and substate search facilities available within Jumna, we rigorously compared the behavior of the different force fields and also of different continuum solvent models. The results, which help to explain trends seen in earlier minimization and molecular dynamics simulations, point to the superiority of the latest Amber parameterization (Parm94) and to a surprising degree of agreement with the Flex force field originally developed for Jumna.