Department of Chemistry, University of Basel, Klingelbergstrasse 80, Basel, Switzerland.
J Chem Inf Model. 2010 Mar 22;50(3):349-57. doi: 10.1021/ci9004404.
Force field parameters are ingredients for realistic atomistic simulations of gas- and condensed-phase systems. Here we discuss the effect of including averaged data from explicit MD simulations in optimizing potential energy functions. It is shown that vibrational frequencies (FeC and CO stretch and FeCO bend) and CO vibrational relaxation times ((v = 1) --> (v = 0) (T(10)) and (v = 2) --> (v = 1) (T(21))) in the active site of CO-bound myoglobin (MbCO) can be well represented with a single set of force field parameters. It is further demonstrated that parameters fitted in a subsystem of MbCO comprising the CO ligand, heme group and proximal histidine, are transferable to investigating the full protein and to providing quantitatively correct results. In particular, it is possible to calculate the CO and FeC stretch and the FeCO bending frequency to within approximately 5%; the relaxation time of the first vibrationally excited state including quantum corrections of T(10) approximately 25 ps is calculated close to the experimental value (17 ps), and the ratio T(10)/T(21) approximately 2 agrees favorably with experimental estimates. In contrast, following the more traditional approach of fitting frequencies from analyzing the Hessian matrix leads to a force field that captures frequencies correctly but not relaxation of vibrations.
力场参数是气相和凝聚相系统的原子模拟的重要组成部分。本文讨论了在优化势能函数时包含显式 MD 模拟的平均数据的效果。结果表明，一氧化碳结合肌红蛋白（MbCO）活性部位的振动频率（FeC 和 CO 伸缩和 FeCO 弯曲）和 CO 振动弛豫时间（（v = 1）-->（v = 0）（T(10)) 和（v = 2）-->（v = 1）（T(21))) 可以用一组力场参数很好地表示。进一步证明，在 MbCO 的子系统中拟合的参数（包括 CO 配体、血红素基团和邻近的组氨酸）可转移到整个蛋白质的研究，并提供定量正确的结果。特别是，可以计算 CO 和 FeC 伸缩以及 FeCO 弯曲频率，误差约为 5%；第一振动激发态的弛豫时间（包括 T(10)的量子修正）约为 25 ps，接近实验值（17 ps），T(10)/T(21)的比值约为 2，与实验估计值相符。相比之下，采用拟合分析 Hessian 矩阵得到的频率的更传统方法得到的力场可以正确捕获频率，但不能捕获振动的弛豫。
