Molecular dynamics simulations of the interaction of wild type human CYP2J2 with arachidonic acid (POSES 5 and 6)

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)See Abelak_etal_Methods.pdf in 10.5281/zenodo.3465884 for details of how the data were produced. Funding and acknowledgments KKA was supported by a PhD studentship from the London Interdisciplinary Biosciences Consortium (LIDo) BBSRC Doctoral Training Partnership programme. The work presented here made use of Emerald, a GPU-accelerated High Performance Computer, made available by the Science and Engineering South Consortium operated in partnership with the STFC Rutherford-Appleton Laboratory