A new web portal for the CHARMM macromolecular modeling package, CHARMMing (CHARMM interface and graphics, http://www.charmming.org), is presented. This tool provides a user-friendly interface for the preparation, submission, monitoring, and visualization of molecular simulations (i.e., energy minimization, solvation, and dynamics). The infrastructure used to implement the web application is described. Two additional programs have been developed and integrated with CHARMMing: GENRTF, which is employed to define structural features not supported by the standard CHARMM force field, and a job broker, which is used to provide a portable method for using grid and cluster computing with CHARMMing. The use of the program is described with three proteins: 1YJP , 1O1O , and 1UFY . Source code is provided allowing CHARMMing to be downloaded, installed, and used by supercomputing centers and research groups that have a CHARMM license. Although no software can replace a scientist's own judgment and experience, CHARMMing eases the introduction of newcomers to the molecular modeling discipline by providing a graphical method for running simulations.

中文翻译：

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CHARMMing：CHARMM 的全新灵活 Web 门户。

介绍了 CHARMM 大分子建模包 CHARMMing （CHARMM 界面和图形，http://www.charmming.org） 的新 Web 门户。该工具为分子模拟（即能量最小化、溶剂化和动力学）的制备、提交、监测和可视化提供了一个用户友好的界面。介绍了用于实现 Web 应用程序的基础结构。已经开发了两个额外的程序并与 CHARMMing 集成：GENRTF，用于定义标准 CHARMM 力场不支持的结构特征，以及一个 job broker，用于提供一种通过 CHARMMing 使用网格和集群计算的可移植方法。该程序的使用用三种蛋白质描述：1YJP 、 1O1O 和 1UFY 。提供源代码，允许拥有 CHARMM 许可证的超级计算中心和研究小组下载、安装和使用 CHARMMing。虽然没有任何软件可以取代科学家自己的判断和经验，但 CHARMMing 通过提供运行模拟的图形方法，简化了分子建模学科新手的介绍。