Preparing molecular coordinate files for molecular dynamics (MD) simulations can be a very time-consuming process. Herein we present the development of a user-friendly program that drastically reduces the time required to prepare these molecular coordinate files for MD software packages such as AmberTools. Our program, known as charge atomtype naming (CAN), creates and uses a library of structures such as amino acid monomers to update the charge, atom type, and name of atoms in any molecular structure (mol2) file. We demonstrate the utility of this new program by rapidly preparing structural files for MD simulations for polypeptides ranging from small molecules to large protein structures. Both native and non-native amino acid residues are easily handled by this new program.

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CAN：简化分子动力学模拟分子坐标文件准备的新程序

为分子动力学 (MD) 模拟准备分子坐标文件可能是一个非常耗时的过程。在这里，我们提出了一个用户友好的程序的开发，它大大减少了为 MD 软件包（如 AmberTools）准备这些分子坐标文件所需的时间。我们的程序称为电荷原子类型命名 (CAN)，它创建并使用氨基酸单体等结构库来更新任何分子结构 (mol2) 文件中的电荷、原子类型和原子名称。我们通过为从小分子到大蛋白质结构的多肽的 MD 模拟快速准备结构文件来证明这个新程序的实用性。这个新程序很容易处理天然和非天然氨基酸残基。