Molecular dynamics simulations of the interaction of mutant human CYP2J2 (R111A) with arachidonic acid (POSES 4-6)

<strong>Description of files in this dataset:</strong> <strong>MD_mutR111A_CYP2J2_AA_StateX_repeatY.zip</strong> : Series of zipped directories for molecular dynamics simulations of arachidonic acid in the active site of the R111A mutant CYP2J2. X is the docking pose number that constitutes the starting point of the simulation (the 6 lowest-energy poses from docking were selected as the starting points of the simulations - this dataset is State(pose) 1). Y is the repeat (each simulation was repeated 3 times, hence there are 3 repeats per pose). Each directory contains the following sub-directories: 001.leap : Amber parameter and coordinate files; PDBs; ligands; leap commands 002.min : Minimisation stage 003.heat : Heating stage 004.equil: Equilibration stage 005.md : Production stage 006.analysis : Basic energy graphs 007.cpptraj: Contains only the file strip.md.nc (Amber trajectories stripped of water in netCDF format)<strong>本数据集文件说明：</strong> <strong>MD_mutR111A_CYP2J2_AA_StateX_repeatY.zip</strong>：该压缩包系列对应细胞色素P450 2J2（CYP2J2）的R111A突变体活性位点内花生四烯酸（arachidonic acid）的分子动力学模拟。其中X为作为模拟起始点的对接构象编号（本次数据集选取对接所得的6个能量最低构象作为模拟起始点，本数据集对应State(构象)1）；Y为重复实验序号，每组构象均重复3次模拟，因此每个构象对应3个重复样本。 每个压缩目录均包含以下子目录： 001.leap：存放Amber参数与坐标文件、PDB（蛋白质数据库）文件、配体文件及leap运行脚本； 002.min：对应能量最小化模拟阶段； 003.heat：对应体系升温阶段； 004.equil：对应体系平衡阶段； 005.md：对应生产级模拟阶段； 006.analysis：包含基础能量曲线图； 007.cpptraj：仅包含strip.md.nc文件，即经Amber处理去除水分子后的netCDF格式分子轨迹文件。