Molecular dynamics simulations of the interaction of mutant human CYP2J2 (R117A) with arachidonic acid (POSES 5-6)

<strong>Description of files in this dataset:</strong> <strong>MD_mutR117A_CYP2J2_AA_StateX_repeatY.zip</strong> : Series of zipped directories for molecular dynamics simulations of arachidonic acid in the active site of the R117A 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)本数据集内的文件说明：<strong>MD_mutR117A_CYP2J2_AA_StateX_repeatY.zip</strong>：该系列压缩目录对应R117A突变型细胞色素P450 2J2（CYP2J2）活性位点内花生四烯酸（arachidonic acid）的分子动力学模拟文件。其中X为作为模拟起始构象的对接姿势编号（本次模拟共选取对接得到的6个最低能量构象作为起始点，本数据集对应State(pose) 1）；Y为重复批次编号（每组姿势的模拟均重复3次，因此每个起始姿势对应3个重复批次）。每个子目录包含如下子文件夹： 001.leap：包含Amber参数文件、坐标文件、PDB文件、配体文件以及tleap预处理命令脚本； 002.min：能量最小化阶段相关文件； 003.heat：升温模拟阶段相关文件； 004.equil：平衡模拟阶段相关文件； 005.md：生产型分子动力学模拟阶段相关文件； 006.analysis：基础能量曲线图等分析结果文件； 007.cpptraj：仅包含strip.md.nc文件，即采用netCDF格式存储的去除水分子的Amber轨迹文件。