Frontiers of Chemical Science and Engineering
>> 2016,
Volume 10,
Issue 2
doi:
10.1007/s11705-016-1572-4
RESEARCH ARTICLE
Validation of polarizable force field parameters for nucleic acids by inter-molecular interactions
. 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.. Department of Ophthalmology, Aerospace Center Hospital, Beijing 100049, China
Accepted: 2016-05-11
Available online: 2016-05-19
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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.
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