Empirical Corrections to the Amber RNA Force Field with Target Metadynamics.
Empirical Corrections to the Amber RNA Force Field with Target Metadynamics.
复制标题
用目标元动力学对琥珀 RNA 力场进行实证修正。
DOI：
10.1021/acs.jctc.6b00299
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发表时间：
2016-06-14
影响因子：
5.5
通讯作者：
Bussi G
中科院分区：
文献类型：
--
作者：
Gil-Ley A;Bottaro S;Bussi G
The computational study of conformational transitions in nucleic acids still faces many challenges. For example, in the case of single stranded RNA tetranucleotides, agreement between simulations and experiments is not satisfactory due to inaccuracies in the force fields commonly used in molecular dynamics simulations. We here use experimental data collected from high-resolution X-ray structures to attempt an improvement of the latest version of the AMBER force field. A modified metadynamics algorithm is used to calculate correcting potentials designed to enforce experimental distributions of backbone torsion angles. Replica-exchange simulations of tetranucleotides including these correcting potentials show significantly better agreement with independent solution experiments for the oligonucleotides containing pyrimidine bases. Although the proposed corrections do not seem to be portable to generic RNA systems, the simulations revealed the importance of the α and ζ backbone angles for the modulation of the RNA conformational ensemble. The correction protocol presented here suggests a systematic procedure for force-field refinement.
