Molecular dynamics simulation data for the publication titled "Tuning of AMPA receptor activation by inhibitory auxiliary subunits and epilepsy-associated disease mutations"

This dataset contains molecular dynamics simulation trajectories and the initial coordinates for the production runs of all simulated structures. Description of the Data and File Structure The data are deposited as a .zip file and organized into 4 folders, each containing MD simulation data for GluA2Glu+RR2b, GluA2-GSG1LGlu+RR2b, GluA2-y5-CNIHGlu+RR2b, and GluA2-y2Glu+CTZ systems. All prodcution trajectory (.nc) files were saved at 200 picosecond intervals starting from the first frame. Please see the table below for the systems and their corresponding topology and trajectory files. System # of Frames Production Length Topology File Trajectory File GluA2Glu+RR2b 2500 500 ns AMPAR_A2_Core_HMR.prmtop AMPAR_A2_Core_traj_prod.nc GluA2-GSG1LGlu+RR2b 2500 500 ns AMPAR_A2_GSG1L.prmtop AMPAR_A2_GSG1L_traj_prod.nc GluA2-y5-CNIHGlu+RR2b 2500 500 ns AMPAR_A2_Y5_CNIH_HMR.prmtop AMPAR_A2_Y5_CNIH_traj_prod.nc GluA2-y2Glu+CTZ 2500 500 ns AMPAR_A2_Y2.prmtop AMPAR_A2_Y2_traj_prod.nc The initial structures (*inpcrd) for the production trajectories, along with their corresponding topology files, are located within each system folder. The topology files use the .prmtop format, and the coordinate files use the .rst7 format. MD production trajectories in binary NetCDF (.nc) format and the coordinate files can be visualized using VMD after loading the corresponding topology file. Analysis of the trajectories can be performed using the CPPTRAJ module of AmberTools and VMD.