RESEARCH ARTICLE

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

  • Liaoran Cao 1 ,
  • Hong Ren 2 ,
  • Jing Miao 1 ,
  • Wei Guo 1 ,
  • Yan Li 1 ,
  • Guohui Li , 1
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  • 1. Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
  • 2. Department of Ophthalmology, Aerospace Center Hospital, Beijing 100049, China

Received date: 31 Dec 2015

Accepted date: 01 Apr 2016

Published date: 19 May 2016

Copyright

2016 Higher Education Press and Springer-Verlag Berlin Heidelberg

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.

Cite this article

Liaoran Cao , Hong Ren , Jing Miao , Wei Guo , Yan Li , Guohui Li . Validation of polarizable force field parameters for nucleic acids by inter-molecular interactions[J]. Frontiers of Chemical Science and Engineering, 2016 , 10(2) : 203 -212 . DOI: 10.1007/s11705-016-1572-4

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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