Liu Hui, Jin Ye, Ding Hanjing
Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
Institute of Functional Nano & Soft Materials (FUNSOM), Soochow University, Suzhou, Jiangsu 215123, China.
Brief Bioinform. 2023 Mar 19;24(2). doi: 10.1093/bib/bbad057.
The preprocessed initial files that feed the molecular dynamics (MD) simulation packages dramatically influence the outcome of the simulations. However, the popular MD simulation packages depend, to a great extent, on the user's experience in the preparation of MD simulation systems. In this work, we present an easy-to-use tool called MDBuilder, a PyMOL plugin that assists researchers in building the starting structures for multiple popular MD simulation packages. MDBuilder is not only designed to assist MD beginners to overcome the steep learning curve by providing a menu-oriented, point-and-click user graphic interface (GUI), but also to provide an alternative way to prepare the input files for some highly scalable CHARMM force field-based MD simulation packages. The platform-independent GUI is implemented as a PyMOL plugin using the Python language, and it has been tested on Windows and Linux platforms. The source code and documentation of MDBuilder can be downloaded freely from https://github.com/HuiLiuCode/MDBuilder under the GNU General Public License.
为分子动力学（MD）模拟程序包提供输入的预处理初始文件会极大地影响模拟结果。然而，流行的MD模拟程序包在很大程度上依赖于用户在准备MD模拟系统方面的经验。在这项工作中，我们展示了一个名为MDBuilder的易用工具，它是一个PyMOL插件，可协助研究人员为多个流行的MD模拟程序包构建初始结构。MDBuilder不仅旨在通过提供面向菜单的、点击式用户图形界面（GUI）来帮助MD初学者克服陡峭的学习曲线，还为一些基于高度可扩展的CHARMM力场的MD模拟程序包提供了一种准备输入文件的替代方法。与平台无关的GUI使用Python语言实现为PyMOL插件，并已在Windows和Linux平台上进行了测试。MDBuilder的源代码和文档可在GNU通用公共许可证下从https://github.com/HuiLiuCode/MDBuilder免费下载。
