Zgarbová Marie, Rosnik Andreana M, Luque F Javier, Curutchet Carles, Jurečka Petr
Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, 17. listopadu 12, Olomouc, 77146, Czech Republic.
Department de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, Barcelona, 08028, Spain.
J Comput Chem. 2015 Sep 30;36(25):1874-84. doi: 10.1002/jcc.24012. Epub 2015 Jul 30.
Recent advances in polarizable force fields have revealed that major reparameterization is necessary when the polarization energy is treated explicitly. This study is focused on the torsional parameters, which are crucial for the accurate description of conformational equilibria in biomolecules. In particular, attention is paid to the influence of polarization on the (i) transferability of dihedral terms between molecules, (ii) transferability between different environments, and (iii) additivity of dihedral energies. To this end, three polarizable force fields based on the induced point dipole model designed for use in AMBER are tested, including two recent ff02 reparameterizations. Attention is paid to the contributions due to short range interactions (1-2, 1-3, and 1-4) within the four atoms defining the dihedral angle. The results show that when short range 1-2 and 1-3 polarization interactions are omitted, as for instance in ff02, the 1-4 polarization contribution is rather small and unlikely to improve the description of the torsional energy. Conversely, when screened 1-2 and 1-3 interactions are included, the polarization contribution is sizeable and shows potential to improve the transferability of parameters between different molecules and environments as well as the additivity of dihedral terms. However, to reproduce intramolecular polarization effects accurately, further fine-tuning of the short range damping of polarization is necessary.
可极化力场的最新进展表明,当明确处理极化能量时,需要进行重大的重新参数化。本研究聚焦于扭转参数,这些参数对于准确描述生物分子中的构象平衡至关重要。特别关注极化对以下方面的影响:(i) 分子间二面角项的可转移性;(ii) 不同环境间的可转移性;(iii) 二面角能量的加和性。为此,测试了基于用于AMBER的诱导点偶极模型设计的三种可极化力场,包括最近的两种ff02重新参数化。研究关注了定义二面角的四个原子内短程相互作用(1-2、1-3和1-4)的贡献。结果表明,例如在ff02中,当忽略短程1-2和1-3极化相互作用时,1-4极化贡献相当小,不太可能改善扭转能量的描述。相反,当包含屏蔽的1-2和1-3相互作用时,极化贡献相当大,显示出改善不同分子和环境间参数可转移性以及二面角项加和性的潜力。然而,为了准确再现分子内极化效应,需要进一步微调极化的短程阻尼。