Departments of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, University of California, Irvine, Irvine, California 92697, United States.
SBP Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States.
J Chem Theory Comput. 2022 Jun 14;18(6):3654-3670. doi: 10.1021/acs.jctc.2c00230. Epub 2022 May 10.
Molecular modeling at the atomic level has been applied in a wide range of biological systems. The widely adopted additive force fields typically use fixed atom-centered partial charges to model electrostatic interactions. However, the additive force fields cannot accurately model polarization effects, leading to unrealistic simulations in polarization-sensitive processes. Numerous efforts have been invested in developing induced dipole-based polarizable force fields. Whether additive atomic charge models or polarizable induced dipole models are used, proper parameterization of the electrostatic term plays a key role in the force field developments. In this work, we present a Python program called for performing atomic multipole parameterizations by reproducing electrostatic potential (ESP) around molecules. provides parameterization schemes for several electrostatic models, including the RESP model with atomic charges for the additive force fields and the RESP-ind and RESP-perm models with additional induced and permanent dipole moments for the polarizable force fields. is a flexible and user-friendly program that can accommodate various needs during force field parameterizations for molecular modeling of any organic molecules.
在原子水平上的分子建模已经被广泛应用于各种生物系统中。广泛采用的加和力场通常使用固定的原子中心部分电荷来模拟静电相互作用。然而，加和力场无法准确地模拟极化效应，导致在极化敏感过程中的模拟不现实。已经投入了大量的努力来开发基于诱导偶极的极化力场。无论是加和原子电荷模型还是极化诱导偶极模型，静电项的正确参数化在力场开发中起着关键作用。在这项工作中，我们提出了一个名为 的 Python 程序，用于通过复制分子周围的静电势能（ESP）来进行原子多极参数化。提供了几种静电模型的参数化方案，包括用于加和力场的原子电荷的 RESP 模型，以及用于极化力场的额外诱导和永久偶极矩的 RESP-ind 和 RESP-perm 模型。是一个灵活且用户友好的程序，可以在任何有机分子的分子建模的力场参数化过程中满足各种需求。
