Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal.
UCIBIO-Applied Molecular Biosciences Unit, BioSIM-Departamento de Biomedicina, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal.
Molecules. 2022 Aug 27;27(17):5524. doi: 10.3390/molecules27175524.
The partitioning of the molecular mechanics (MM) energy in calculations involving biomolecular systems is important to identify the source of major stabilizing interactions, e.g., in ligand-protein interactions, or to identify residues with considerable contributions in hybrid multiscale calculations, i.e., quantum mechanics/molecular mechanics (QM/MM). Here, we describe Energy Split, a software program to calculate MM energy partitioning considering the AMBER Hamiltonian and parameters. Energy Split includes a graphical interface plugin for VMD to facilitate the selection of atoms and molecules belonging to each part of the system. Energy Split is freely available at or can be easily installed through the VMD Store.
在涉及生物分子系统的计算中，对分子力学（MM）能量进行分区对于确定主要稳定相互作用的来源（例如，在配体-蛋白质相互作用中）或识别在混合多尺度计算（即量子力学/分子力学（QM/MM））中具有重要贡献的残基非常重要。在这里，我们描述了 Energy Split，这是一个用于计算考虑 AMBER 哈密顿量和参数的 MM 能量分区的软件程序。Energy Split 包括一个用于 VMD 的图形界面插件，以方便选择属于系统各个部分的原子和分子。Energy Split 可在或通过 VMD Store 轻松安装。
