Wang Lee-Ping, McKiernan Keri A, Gomes Joseph, Beauchamp Kyle A, Head-Gordon Teresa, Rice Julia E, Swope William C, Martínez Todd J, Pande Vijay S
Department of Chemistry, University of California, Davis , Davis, California 95616, United States.
Department of Chemistry, Stanford University , Stanford, California 94305, United States.
J Phys Chem B. 2017 Apr 27;121(16):4023-4039. doi: 10.1021/acs.jpcb.7b02320. Epub 2017 Apr 6.
The increasing availability of high-quality experimental data and first-principles calculations creates opportunities for developing more accurate empirical force fields for simulation of proteins. We developed the AMBER-FB15 protein force field by building a high-quality quantum chemical data set consisting of comprehensive potential energy scans and employing the ForceBalance software package for parameter optimization. The optimized potential surface allows for more significant thermodynamic fluctuations away from local minima. In validation studies where simulation results are compared to experimental measurements, AMBER-FB15 in combination with the updated TIP3P-FB water model predicts equilibrium properties with equivalent accuracy, and temperature dependent properties with significantly improved accuracy, in comparison with published models. We also discuss the effect of changing the protein force field and water model on the simulation results.
高质量实验数据和第一性原理计算的可得性不断提高,为开发更精确的用于蛋白质模拟的经验力场创造了机会。我们通过构建一个由全面的势能扫描组成的高质量量子化学数据集,并使用ForceBalance软件包进行参数优化,开发了AMBER-FB15蛋白质力场。优化后的势能面允许从局部最小值产生更显著的热力学涨落。在将模拟结果与实验测量进行比较的验证研究中,与已发表的模型相比,AMBER-FB15与更新的TIP3P-FB水模型相结合,预测平衡性质具有同等的准确性,预测温度相关性质的准确性则显著提高。我们还讨论了改变蛋白质力场和水模型对模拟结果的影响。