CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations
CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations
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DOI：
10.1002/jcc.10355
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发表时间：
2004-01-15
影响因子：
3
通讯作者：
Brooks, CL
中科院分区：
文献类型：
--
作者：
Patel, S;Brooks, CL
提出了将最终应用于蛋白质模拟的第一代波动电荷力场。静电模型参数、原子硬度和电负性通过拟合小分子在模拟水偶极子的偶极探针扰动下基于dft的电荷响应来参数化。基于CHARMM原子分型方案的原子非键参数是通过同时优化纯散装液体的真空水溶质几何形状和能量（一组小有机分子）以及凝聚相性质（密度和蒸发焓）来确定的。真空溶质水的几何形状，特别是氢键距离，适合于0.19埃的均方根误差，而二聚化能适合于0.98千卡/摩尔均方根误差。所研究液体的性质包括体液结构和极化。FQ模型确实显示了分子偶极矩相对于气相向更高值移动的凝聚相效应。在氢键液体的情况下，由于偶极相互作用的增强，FQ液体也表现出更强的相关性，这是由对能量分布中向低能量转移所证明的。作为模拟溶剂化肽/蛋白质系统的一步，我们展示了从散装TIP4P-FQ水中NMA的简短模拟结果。正如预期的那样，NMA有一个非平凡的偶极矩增强（尽管定量精度难以评估）。此外，在溶质附近的水分子偶极矩的分布向更大的值移动了0.1-0.2 Debye，与先前报道的工作保持一致。(C) 2003 Wiley期刊有限公司
A first-generation fluctuating charge (FQ) force field to be ultimately applied for protein simulations is presented. The electrostatic model parameters, the atomic hardnesses, and electronegativities, are parameterized by fitting to DFT-based charge responses of small molecules perturbed by a dipolar probe mimicking a water dipole. The nonbonded parameters for atoms based on the CHARMM atom-typing scheme are determined via simultaneously optimizing vacuum water-solute geometries and energies (for a set of small organic molecules) and condensed phase properties (densities and vaporization enthalpies) for pure bulk liquids. Vacuum solute-water geometries, specifically hydrogen bond distances, are fit to 0.19 Angstrom r.m.s. error, while dimerization energies are fit to 0.98 kcal/mol r.m.s. error. Properties of the liquids studied include bulk liquid structure and polarization. The FQ model does indeed show a condensed phase effect in the shifting of molecular dipole moments to higher values relative to the gas phase. The FQ liquids also appear to be more strongly associated, in the case of hydrogen bonding liquids, due to the enhanced dipolar interactions as evidenced by shifts toward lower energies in pair energy distributions. We present results from a short simulation of NMA in bulk TIP4P-FQ water as a step towards simulating solvated peptide/protein systems. As expected, there is a nontrivial dipole moment enhancement of the NMA (although the quantitative accuracy is difficult to assess). Furthermore, the distribution of dipole moments of water molecules in the vicinity of the solutes is shifted towards larger values by 0.1-0.2 Debye in keeping with previously reported work. (C) 2003 Wiley Periodicals, Inc.