Parameters of monovalent ions in the AMBER-99 forcefield: Assessment of inaccuracies and proposed improvements
Parameters of monovalent ions in the AMBER-99 forcefield: Assessment of inaccuracies and proposed improvements
复制标题
DOI：
10.1021/jp0765392
复制
发表时间：
2007-10-18
影响因子：
3.3
通讯作者：
Pappu, Rohit V.
中科院分区：
文献类型：
--
作者：
Chen, Alan A.;Pappu, Rohit V.
琥珀色99力场使用的单价离子参数显示出在强1：1电解质的分子动力学模拟中表现出物理上不准确的行为。这些错误来自AQVIST阳离子参数的临时适应。结果是在浓度低于溶解度极限的浓度下快速形成了大型的非物理簇。观察到的非物理行为对在高电荷聚合物（如核酸）周围进行模拟离子构成了严重的挑战。在这种交流中，我们解释了这种非物理行为的来源。为了促进持续使用流行的琥珀色参数，我们开了一个简单的修复程序，其中AQVIST的阳离子和阴离子与琥珀色力场一起用于核酸。对该策略的初步测试表明，所提出的固定是合理的，并且很可能可以推广用于模拟弥漫性和特定离子与核酸的结合。
The monovalent ion parameters used by the AMBER-99 forcefield are shown to exhibit physically inaccurate behavior in molecular dynamics simulations of strong 1:1 electrolytes. These errors arise from an ad hoc adaptation of Aqvist's cation parameters. The result is the rapid formation of large, unphysical clusters at concentrations that are well below solubility limits. The observed unphysical behavior poses a serious challenge for simulating ions around highly charged polymers such as nucleic acids. In this communication, we explain the source of this unphysical behavior. To facilitate the continued use of the popular AMBER parameters, we prescribe a simple fix whereby Aqvist's cations and anions are used in conjunction with the AMBER forcefield for nucleic acids. A preliminary test of this strategy suggests that the proposed fix is reasonable and is likely to be generalizable for simulating diffuse and specific ion binding to nucleic acids.