Department of Computational Biophysics and Bioinformatics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University ul. Gronostajowa 7, 30-387 Cracow, Poland.
Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University ul. Gronostajowa 7, 30-387 Cracow, Poland.
Chem Phys Lipids. 2022 Jul;245:105203. doi: 10.1016/j.chemphyslip.2022.105203. Epub 2022 Apr 7.
Lipids play a central role within the cell. They not only encompass it but are also engaged in many processes such as cellular transport and energy production. Despite ongoing advances in experimental studies, computer simulations are a viable method to trace their behavior at the atomic level and on an elusive time scale. In molecular modeling studies, the quality of the obtained results is associated with the considered force field and its parameters. In the present work, the authors have investigated the procedure of partial charges fitting on the example of a triacetin molecule, containing chemical moieties present in the glycerol backbone. The goal of the study was to validate assigned partial charges based on the quality of the torsion profiles using optimally assigned torsional coefficients and reproduction of the condensed phase properties of triacetin. We applied various approaches and noticed a significant improvement in the parameterization of triacetin compared to the original one. The results showed that it is important to take into account the intermolecular interactions in the partial charges fitting procedure to obtain good quality validation results.
脂质在细胞中起着核心作用。它们不仅包围着细胞，还参与许多过程，如细胞运输和能量产生。尽管实验研究不断取得进展，但计算机模拟是一种可行的方法，可以在原子水平和难以捉摸的时间尺度上追踪它们的行为。在分子建模研究中，获得的结果的质量与所考虑的力场及其参数有关。在本工作中，作者以含有甘油主链中化学部分的三醋酸甘油酯分子为例，研究了部分电荷拟合的程序。研究的目的是基于使用最佳分配的扭转系数和再现三醋酸甘油酯的凝聚相性质来验证所分配的部分电荷。我们应用了各种方法，并注意到与原始参数相比，三醋酸甘油酯的参数化有了显著的改进。结果表明，在部分电荷拟合过程中考虑分子间相互作用对于获得高质量的验证结果很重要。
