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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

✍ Scribed by P. Hobza; F. Hubálek; M. Kabeláč; P. Mejzlík; J. Šponer; J. Vondrášek

Publisher: Elsevier Science
Year: 1996
Tongue: English
Weight: 287 KB
Volume: 257
Category: Article
ISSN: 0009-2614
DOI: 10.1016/0009-2614(96)00537-4

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✦ Synopsis

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.

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✍ Hobza, Pavel; Kabel�?, Martin; ?poner, Ji?�; Mejzl�k, Petr; Vondr�?ek, Ji?� 📂 Article 📅 1997 🏛 John Wiley and Sons 🌐 English ⚖ 373 KB 👁 2 views

## PERFORMANCE METHODS FOR INTERACTION OF DNA BASES exhibited by AMBER 4.1 with the force field of Cornell et al. The SCFD method, tested for H-bonded pairs only, exhibited stabilization energies that were too large. Semiempirical quantum chemical methods gave poor agreement with MP2 values in the