Molecular dynamics simulations of the interaction of wild type human CYP2J2 with arachidonic acid (POSES 1 and 2)

Description of files in this dataset:

MD_wt_CYP2J2_AA_StateX_repeatY.zip : Series of zipped directories for molecular dynamics simulations of arachidonic acid in the active site of wild type 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 4 times, hence there are 4 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)