Evaluating the Performance of the ff99SB Force Field Based on NMR Scalar Coupling Data
Evaluating the Performance of the ff99SB Force Field Based on NMR Scalar Coupling Data
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DOI：
10.1016/j.bpj.2009.04.063
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发表时间：
2009-08-05
影响因子：
3.4
通讯作者：
Simmerling, Carlos
中科院分区：
文献类型：
--
作者：
Wickstrom, Lauren;Okur, Asim;Simmerling, Carlos
力场验证对于识别当前模型中的弱点和开发更准确的生物分子模型至关重要。核磁共振耦合和弛豫方法已被用来有效地诊断许多现有力场的优缺点。利用ff99SB力场进行的研究表明，实验和计算的有序参数以及剩余偶极子计算结果非常吻合。然而，最近的研究表明，ff99SB与短聚丙氨酸的j偶联常数的一致性较差。我们在TIP3P和TIP4P-Ew溶剂模型中对Ala(3)和Ala(5)进行了广泛的复制交换分子动力学模拟。我们的结果表明，ff99SB的性能是目前可用的模型中最好的。此外，用TIP4P-Ew模型模拟得到的标量耦合常数比用TIP3P模型得到的数值略有提高。尽管总体上非常一致，但数据显示了可能改进的领域。
Force-field validation is essential for the identification of weaknesses in current models and the development of more accurate models of biomolecules. NMR coupling and relaxation methods have been used to effectively diagnose the strengths and weaknesses of many existing force fields. Studies using the ff99SB force field have shown excellent agreement between experimental and calculated order parameters and residual dipolar calculations. However, recent studies have suggested that ff99SB demonstrates poor agreement with J-coupling constants for short polyalanines. We performed extensive replica-exchange molecular-dynamics simulations on Ala(3) and Ala(5) in TIP3P and TIP4P-Ew solvent models. Our results suggest that the performance of ff99SB is among the best of currently available models. In addition, scalar coupling constants derived from simulations in the TIP4P-Ew model show a slight improvement over those obtained using the TIP3P model. Despite the overall excellent agreement, the data suggest areas for possible improvement.