PDB2DAT：使用 Python、Rdkit 和 Pysimm 从 PDB 分子系统自动生成 LAMMPS 数据文件

IF 1.3 Q3 COMPUTER SCIENCE, SOFTWARE ENGINEERING

Software Impacts Pub Date : 2024-05-01 DOI:10.1016/j.simpa.2024.100656

Eli I. Assaf , Xueyan Liu , Peng Lin , Sandra Erkens

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引用次数: 0

摘要

Pdb2dat 是用 Python 开发的一款开源、独立的实用程序，可帮助将 PDB 文件转换为 LAMMPS 数据文件，满足从初始原子构型初始化原子模拟的需要。它能从 PDB 文件中提取分子细节，使用 Rdkit 和 Xyz2mol 进行成键分析和三维构象生成，并使用 Pysimm 分配力场类型和电荷。pdb2dat 设计轻巧，完全采用 Pythonic 语言，适合在有权限限制的高通量环境中使用。输出结果详细说明了用于 MD 模拟的系统拓扑结构，大大简化了研究人员通过 LAMMPS 探索材料现象所需的准备步骤。

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PDB2DAT: Automating LAMMPS data file generation from PDB molecular systems using Python, Rdkit, and Pysimm

Pdb2dat, developed in Python, is an open-source, self-contained utility that facilitates the conversion of PDB files into LAMMPS data files, catering to the need of initializing atomistic simulation from initial atomic configurations. It extracts molecular details from PDB files, uses Rdkit and Xyz2mol for bonding analysis and 3D conformer generation, and uses Pysimm for assigning force field types and charges. Designed to be lightweight and fully Pythonic, pdb2dat is suitable for use in privilege-limited high-throughput environments. The output details system topologies for use in MD simulations, significantly simplifying the preparatory steps needed by researchers to explore materials phenomena through LAMMPS.

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来源期刊

Software Impacts Software

CiteScore

2.70

自引率

9.50%

发文量

审稿时长

16 days