RNA Stability Under Different Combinations of Amber Force Fields and Solvation Models
RNA Stability Under Different Combinations of Amber Force Fields and Solvation Models
复制标题
琥珀力场和溶剂化模型不同组合下的 RNA 稳定性
DOI：
10.1080/07391102.2010.10507372
复制
发表时间：
2010-12-01
影响因子：
4.4
通讯作者：
Xiao, Yi
中科院分区：
文献类型：
--
作者：
Gong, Zhou;Zhao, Yunjie;Xiao, Yi
在生物分子的分子动力学模拟中，力场与溶剂的适当匹配是获得正确结果的关键。这个问题已经深入研究了蛋白质，但还没有研究RNA。本文采用标准分子动力学和复制交换分子动力学对不同琥珀力场参数（ff98、ff99和ff99bsc0）组合和通用Born隐式溶剂模型（igb1、igb2和igb5）下RNA的稳定性进行了一系列测试。发现只有含有igb1的ff98和ff99bsc0能保持RNA发夹和双工的天然构象。我们的结果表明ff98加igb1可能是分子动力学模拟RNA动力学的合理选择。
The proper matching of force field and solvent is critical to obtain correct result in molecular dynamics simulation of bio-molecules. This problem has been intensively investigated for protein but not for RNA yet. In this paper, we use standard molecular dynamics and replica exchange molecular dynamics to take a series of tests on the RNA stability under different combinations of Amber force field parameters (ff98, ff99 and ff99bsc0) and the general Born implicit solvent models (igb1, igb2 and igb5). It is found that only ff98 and ff99bsc0 with igb1 can keep the native conformations of RNA hairpin and duplex. Our results suggest that ff98 plus igb1 may be reasonable choice for molecular dynamics simulation of RNA dynamics.