Improved Force Field Parameters Lead to a Better Description of RNA Structure

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• 作者：Christina Bergonzo ; Thomas E. Cheatham III
• 刊名：Journal of Chemical Theory and Computation
• 出版年：2015
• 出版时间：September 8, 2015
• 年：2015
• 卷：11
• 期：9
• 页码：3969-3972
• 全文大小：238K
• ISSN：1549-9626

文摘

We compare the performance of two different RNA force fields in four water models in simulating the conformational ensembles r(GACC) and r(CCCC). With the increased sampling facilitated by multidimensional replica exchange molecular dynamics (M-REMD), populations are compared to NMR data to evaluate force field reliability. The combination of AMBER ff12 with vdW_bb modifications and the OPC water model produces results in quantitative agreement with the NMR ensemble that have eluded us to date.