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

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.

Graphical abstract

Keywords

nucleic acid / polarizable force field / AMOEBA

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Acknowledgements

This work was financially supported by the National Nature Science Foundation of China (Grant Nos. 21573217, 31370714, and 91430110).

Electronic Supplementary Material

Supplementary material is available in the online version of this article at http://dx.doi.org/10.1007/s11705-016-1572-4 and is accessible for authorized users.

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2016 Higher Education Press and Springer-Verlag Berlin Heidelberg