Effective Fragment Potentials for Flexible Molecules: Transferability of Parameters and Amino Acid Database
Effective Fragment Potentials for Flexible Molecules: Transferability of Parameters and Amino Acid Database
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柔性分子的有效片段潜力：参数和氨基酸数据库的可转移性
DOI：
10.1021/acs.jctc.0c00758
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发表时间：
2020
影响因子：
5.5
通讯作者：
Slipchenko, Lyudmila V.
中科院分区：
文献类型：
--
作者：
Kim, Yongbin;Bui, Yen;Tazhigulov, Ruslan N.;Bravaya, Ksenia B.;Slipchenko, Lyudmila V.
对非共价相互作用的准确而有效的描述是生物和材料系统预测建模的关键。有效碎片势 (EFP) 是一种从头开始的力场，可将分子系统的非共价相互作用以物理意义的方式分解为库仑、极化、色散和交换排斥分量。 EFP 模拟协议包括两个步骤，通过对每个单独片段进行一系列 ofab 初始计算来准备分子片段的参数，并根据准备的参数计算整个分子系统的相互作用能和性质。由于片段参数（分布式多极、极化率、局域波函数等）取决于片段几何形状，因此如果片段几何形状发生变化（例如在分子系统的热波动期间），EFP 方法的直接应用需要重新计算每个片段的参数。因此，重新计算片段参数很容易成为计算和人类瓶颈，并导致模拟协议效率下降。这里探讨了一种替代方法，其中片段参数根据不同的片段几何形状进行调整，称为“灵活 EFP”。参数调整基于与片段原子相关的局部坐标系的平移和旋转。该协议在从隐花色素蛋白的分子动力学快照中提取的氨基酸二聚体的广泛基准上进行了验证。开发了标准氨基酸的参数数据库，以自动化蛋白质中灵活的 EFP 模拟。为了证明灵活 EFP 在大规模蛋白质模拟中的适用性，计算了隐花色素蛋白的发光黄素发色团的结合能以及垂直电子电离和电子附着能。使用灵活 EFP 获得的结果与标准 EFP 程序非常一致，但计算成本显着降低。
An accurate but efficient description of noncovalent interactions is a key to predictive modeling of biological and materials systems. The effective fragment potential (EFP) is anab initio-based force field that provides a physically meaningful decomposition of noncovalent interactions of a molecular system into Coulomb, polarization, dispersion, and exchange-repulsion components. An EFP simulation protocol consists of two steps, preparing parameters for molecular fragments by a series ofab initiocalculations on each individual fragment, and calculation of interaction energy and properties of a total molecular system based on the prepared parameters. As the fragment parameters (distributed multipoles, polarizabilities, localized wave function,etc.) depend on a fragment geometry, straightforward application of the EFP method requires recomputing parameters of each fragment if its geometry changes, for example, during thermal fluctuations of a molecular system. Thus, recomputing fragment parameters can easily become both computational and human bottlenecks and lead to a loss of efficiency of a simulation protocol. An alternative approach, in which fragment parameters are adjusted to different fragment geometries, referred to as “flexible EFP”, is explored here. The parameter adjustment is based on translations and rotations of local coordinate frames associated with fragment atoms. The protocol is validated on extensive benchmark of amino acid dimers extracted from molecular dynamics snapshots of a cryptochrome protein. A parameter database for standard amino acids is developed to automate flexible EFP simulations in proteins. To demonstrate applicability of flexible EFP in large-scale protein simulations, binding energies and vertical electron ionization and electron attachment energies of a lumiflavin chromophore of the cryptochrome protein are computed. The results obtained with flexible EFP are in a close agreement with the standard EFP procedure but provide a significant reduction in computational cost.