ABILITY OF EMPIRICAL POTENTIALS (AMBER, CHARMM, CVFF, OPLS, POLTEV) AND SEMI-EMPIRICAL QUANTUM CHEMICAL METHODS (AM1, MNDO/M, PM3) TO DESCRIBE H-BONDING IN DNA BASE PAIRS - COMPARISON WITH AB INITIO RESULTS

摘要

Various empirical potentials (AMBER 3.0, AMBER 4.1, CHARMM 23, CVFF, OPLS, Poltev) and semi-empirical quantum chemical methods (AM1, PM3, MNDO/M) were tested to reproduce the ab initio MP2 stabilization energies of DNA H-bonded base pairs (26 different base pairs). The best performance of an empirical potential is exhibited by AMBER 4.1 and of semi-empirical quantum chemical methods by MNDO/M. [References: 20]