Underlying data for "The role of electrostatics in enzymes: do biomolecular force fields reflect protein electric fields?"

This dataset contains code, data, trajectories, and figures used in the article "The role of electrostatics in enzymes: do biomolecular force fields reflect protein electric fields?". Contents: code/* - Code used to calculate electric fields from simulation trajectories with either polarizable or additive force fields data/* - Electric fields calculated for the CypA WT cis, WT trans, R55A cis, and R55A trans systems, with AMOEBA, Amber, or Charmm force fields. Each subfolder also includes a set of structural coordinates extracted at 2.5 ns intervals from the first simulation trajectory and used to calculate ONETEP DFT electric fields. figures/* - Underlying data and scripts used to create all figures and movies used in the article. trajectories/* - Simulation trajectories of the CypA WT cis, WT trans, R55A cis, and R55A trans systems Where appropriate, README files include instructions for regenerating data used in the article, and details of the Python packages and other software used to generate data are available in Dependencies.txt本数据集包含论文《酶中的静电作用：生物分子力场能否准确反映蛋白质电场？》中所使用的代码、数据、模拟轨迹与图表。具体内容如下： 1. code/*：存放用于从极化力场或加和型力场的模拟轨迹中计算电场的代码。 2. data/*：包含针对CypA WT顺式、WT反式、R55A顺式、R55A反式体系，采用AMOEBA、Amber或Charmm力场计算得到的电场数据。每个子文件夹还附带一组从首条模拟轨迹中以2.5纳秒为间隔提取的结构坐标，用于计算ONETEP密度泛函理论（DFT）电场。 3. figures/*：存放论文中所有图表与动图的原始数据及生成脚本。 4. trajectories/*：包含CypA WT顺式、WT反式、R55A顺式、R55A反式体系的模拟轨迹。 在适用场景下，README文件将提供论文所用数据的复现指南，生成数据所需的Python包及其他软件的详细信息可在Dependencies.txt中查阅。