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2016 1

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AMOEBA 1

nucleic acid 1

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Validation of polarizable force field parameters for nucleic acids by inter-molecular interactions

Liaoran Cao,Hong Ren,Jing Miao,Wei Guo,Yan Li,Guohui Li

Frontiers of Chemical Science and Engineering 2016, Volume 10, Issue 2, Pages 203-212 doi: 10.1007/s11705-016-1572-4

Abstract: Modeling structural and thermodynamic properties of nucleic acids has long been a challenge in the development of force fields. Polarizable force fields are a new generation of potential functions to take charge redistribution and induced dipole into account, and have been proved to be reliable to model small molecules, polypeptides and proteins, but their use on nucleic acids is still rather limited. In this article, the interactions between nucleic acids and a small molecule or ion were modeled by AMOEBAbio09, a modern polarizable force field, and conventional non-polarizable AMBER99sb and CHARMM36 force fields. The resulting intermolecular interaction energies were compared with those calculated by ab initio quantum mechanics methods. Although the test is not sufficient to prove the reliability of the polarizable force field, the results at least validate its capability in modeling energetics of static configurations, which is one basic component in force field parameterization.

Keywords： nucleic acid polarizable force field AMOEBA