Institute of Science, Department of Chemistry, Dicle University, 21280 Diyarbakir, Turkey.
Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Dicle University, 21280 Diyarbakir Turkey.
Molecules. 2020 May 8;25(9):2196. doi: 10.3390/molecules25092196.
Boric acid, borate esters, and hydroxy derivatives are biologically active molecules. Thus, performing molecular dynamics simulations of these molecules is vital in terms of drug design, but it is difficult to find directly generated Amber parameters based on an ab initio method for these kinds of molecules in the literature. In this study, Amber parameters for such molecules containing boron were generated based on ab initio calculations using the paramfit program, which applies a combination of genetic and simplex algorithms, and the Visual Force Field Derivation Toolkit (VFFDT) program containing the Seminario method. The minimized structure, after obtaining novel parameters and the sander program, was compared with the experimental crystallographic structures, and it was observed that the root-mean-square deviation (RMSD) value between the experimental structure and minimized structure agreed reasonably well. In addition, the molecule was heated, and the molecular dynamics simulation was successfully obtained with the novel parameters.
硼酸、硼酸酯和羟基衍生物是具有生物活性的分子。因此，对这些分子进行分子动力学模拟在药物设计方面至关重要，但在文献中很难找到基于从头计算方法为这些类型的分子直接生成的 Amber 参数。在这项研究中，使用 paramfit 程序（该程序应用遗传和单纯形算法的组合）和包含 Seminario 方法的 Visual Force Field Derivation Toolkit (VFFDT) 程序，基于从头计算为包含硼的此类分子生成了 Amber 参数。获得新参数和 sander 程序后，对最小化结构进行了比较，与实验晶体结构，观察到实验结构和最小化结构之间的均方根偏差 (RMSD) 值相当吻合。此外，对分子进行加热，并使用新参数成功获得了分子动力学模拟。
