Software News and Updates A Toolkit to Assist ONIOM Calculations

Abstract: A general procedure for quantum mechanics and molecular mechanics (QM/MM) studies on biochemi-cal systems is outlined, and a collection of PERL scripts to facilitate ONIOM-type QM/MM calculations is described. This toolkit is designed to assist in the different stages of an ONIOM QM/MM study of biomolecules, including input file preparation and checking, job monitoring, production calculations, and results analysis. An itera-tive procedure for refitting the partial charges of QM region atoms is described and yields a more accurate treatment of the electrostatic interaction between QM and MM regions during QM/MM calculations. The toolkit fully supports this partial charge-refitting procedure. By using this toolkit for file conversions, structure manipulation, input sanity checks, parameter lookup, charge refitting, tracking optimizations, and analyzing results, QM/MM studies of large size biochemical systems can be much more convenient and practical