Dong Chen, Yong-Zhi Li, Zhi-Chao Wei, Bo Liu
Institute of Photo-Biophysics, Physics and Electronics Department, Henan University, 475004, Kaifeng, China.
J Mol Model. 2014 Jun;20(6):2279. doi: 10.1007/s00894-014-2279-4. Epub 2014 May 27.
Monte-Carlo conformational searches with four kinds of force fields (AMBER94, MM3*, MMFFs, and OPLS-2005) were performed on glycylglycine (GlyGly), deprotonated glycylglycine (GlyGly(-)), glycylglycine chloride anion complex (GlyGly · Cl(-)), glycylglycine sodium cation complex (GlyGly · Na(+)) and glycylglycine dihydrate [GlyGly · (H2O)2]. Combined with Hartree-Fock (HF) and second-order Møller-Plesset (MP2) optimizations, conformations within an energy of 20 kJ mol(-1) were predicted. After MP2 calculations, the geometries and relative energies of the predicted structures were the same regardless of the force field used. Therefore, the performance of different force fields reflects mainly the conformational search process. For GlyGly, there was practically no difference among the four force fields. Due to the complex hydrogen bonding network when involving water, the total number of resulting conformers for GlyGly · (H2O)2 increased drastically. Moreover, the MMFFs force field fared best in finding the global minimum compared to the remaining three force fields. In describing hydrogen bonded and inter-molecular complexes, we recommend application of the MMFFs and AMBER94 force fields. Furthermore, the MMFFs and OPLS-2005 force fields have a good description of electrostatic interactions. This work will contribute to helping the reader make an optimal choice of force field, taking into account the latter's strengths and limitations.
使用四种力场（AMBER94、MM3*、MMFFs和OPLS - 2005）对甘氨酰甘氨酸（GlyGly）、去质子化甘氨酰甘氨酸（GlyGly(-)）、甘氨酰甘氨酸氯阴离子复合物（GlyGly·Cl(-)）、甘氨酰甘氨酸钠阳离子复合物（GlyGly·Na(+)）和甘氨酰甘氨酸二水合物[GlyGly·(H2O)2]进行了蒙特卡罗构象搜索。结合哈特里 - 福克（HF）和二阶莫勒 - 普莱塞特（MP2）优化，预测了能量在20 kJ mol(-1)以内的构象。经过MP2计算后，无论使用何种力场，预测结构的几何形状和相对能量都是相同的。因此，不同力场的性能主要反映在构象搜索过程中。对于GlyGly，这四种力场之间实际上没有差异。由于涉及水时存在复杂的氢键网络，GlyGly·(H2O)2产生的构象总数急剧增加。此外，与其余三种力场相比，MMFFs力场在寻找全局最小值方面表现最佳。在描述氢键和分子间复合物时，我们建议应用MMFFs和AMBER94力场。此外，MMFFs和OPLS - 2005力场对静电相互作用有很好的描述。这项工作将有助于读者在考虑力场的优势和局限性的情况下，做出最佳的力场选择。
