A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6
A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6
复制标题
DOI：
10.1002/jcc.20090
复制
发表时间：
2004-10-01
影响因子：
3
通讯作者：
Van Gunsteren, WF
中科院分区：
文献类型：
--
作者：
Oostenbrink, C;Villa, A;Van Gunsteren, WF
连续参数化的GROMOS力场已成功地用于模拟生物分子系统在很长一段时间。随着时间的推移，计算能力的不断扩展，使得以更高的精度计算越来越多种类的分子系统的更多性质成为可能。这导致了GROMOS力场的经常性参数化，所有这些都旨在与实验数据更好地吻合。在这里，我们报告的结果，最新的，广泛的重新参数化的GROMOS力场。与其他生物分子力场的参数化相反，GROMOS力场的参数化主要基于再现一系列化合物的水合和非极性溶剂化的自由基。之所以选择这种方法，是因为极性和非极性环境之间的相对溶剂化自由焓是许多感兴趣的生物分子过程中的关键特性，例如蛋白质折叠、生物分子缔合、膜形成和膜上的运输。最新的参数集，53A5和53A6，通过第一次拟合来优化，以再现一系列小极性分子的纯液体的热力学性质和氨基酸类似物在环己烷中的无溶剂化的热力学性质（53A5）。然后调节部分装料以在水中再现无水合的水化产物（53A6）。这两个参数集都有完整的文档记录，并讨论了这些参数集和以前的参数集之间的差异。(C)2004 Wiley Periodicals，Inc.
Successive parameterizations of the GROMOS force field have been used successfully to simulate biomolecular systems over a long period of time. The continuing expansion of computational power with time makes it possible to compute ever more properties for an increasing variety of molecular systems with greater precision. This has led to recurrent parameterizations of the GROMOS force field all aimed at achieving better agreement with experimental data. Here we report the results of the latest, extensive reparameterization of the GROMOS force field. In contrast to the parameterization of other biomolecular force fields, this parameterization of the GROMOS force field is based primarily on reproducing the free enthalpies of hydration and apolar solvation for a range of compounds. This approach was chosen because the relative free enthalpy of solvation between polar and apolar environments is a key property in many biomolecular processes of interest, such as protein folding, biomolecular association, membrane formation, and transport over membranes. The newest parameter sets, 53A5 and 53A6, were optimized by first fitting to reproduce the thermodynamic properties of pure liquids of a range of small polar molecules and the solvation free enthalpies of amino acid analogs in cyclohexane (53A5). The partial charges were then adjusted to reproduce the hydration free enthalpies in water (53A6). Both parameter sets are fully documented, and the differences between these and previous parameter sets are discussed. (C) 2004 Wiley Periodicals, Inc.