UCIBIO@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre s/n, Porto, 4169-007, Portugal.
J Comput Chem. 2018 Jul 15;39(19):1344-1353. doi: 10.1002/jcc.25189. Epub 2018 Feb 21.
The notable advances obtained by computational (bio)chemistry provided its widespread use in many areas of science, in particular, in the study of reaction mechanisms. These studies involve a huge number of complex calculations, which are often carried out using the Gaussian suite of programs. The preparation of input files and the analysis of the output files are not easy tasks and often involve laborious and complex steps. Taking this into account, we developed molUP: a VMD plugin that offers a complete set of tools that enhance the preparation of QM and ONIOM (QM/MM, QM/QM, and QM/QM/MM) calculations. The starting structures for these calculations can be imported from different chemical formats. A set of tools is available to help the user to examine or modify any geometry parameter. This includes the definition of layers in ONIOM calculations, choosing fixed atoms during geometry optimizations, the recalculation or adjustment of the atomic charges, performing SCANs or IRC calculations, etc. molUP also extracts the geometries from the output files as well as the energies of each of them. All of these tasks are performed in an interactive GUI that is extremely helpful for the user. MolUP was developed to be easy to handle by inexperienced users, but simultaneously to be a fast and flexible graphical interface to allow the advanced users to take full advantage of this plugin. The program is available, free of charges, for macOS, Linux, and Windows at the PortoBioComp page https://www.fc.up.pt/PortoBioComp/database/doku.php?id=molup. © 2018 Wiley Periodicals, Inc.
计算（生物）化学取得的显著进展使其在科学的许多领域得到广泛应用，特别是在反应机制的研究中。这些研究涉及大量复杂的计算，这些计算通常使用 Gaussian 程序套件来进行。输入文件的准备和输出文件的分析都不是简单的任务，通常涉及繁琐和复杂的步骤。考虑到这一点，我们开发了 molUP：一个 VMD 插件，提供了一套完整的工具，增强了 QM 和 ONIOM（QM/MM、QM/QM 和 QM/QM/MM）计算的准备工作。这些计算的起始结构可以从不同的化学格式导入。有一组工具可供用户使用，帮助检查或修改任何几何参数。这包括在 ONIOM 计算中定义层、在几何优化过程中选择固定原子、重新计算或调整原子电荷、执行 SCAN 或 IRC 计算等。molUP 还从输出文件中提取几何形状以及它们各自的能量。所有这些任务都在一个交互式 GUI 中完成，这对用户非常有帮助。molUP 的开发目的是让没有经验的用户易于操作，同时也让它成为一个快速灵活的图形界面，让高级用户能够充分利用这个插件。该程序可在 macOS、Linux 和 Windows 上免费获得，网址为 https://www.fc.up.pt/PortoBioComp/database/doku.php?id=molup。 © 2018 威利期刊公司
