Molecular dynamics simulation data for the publication titled "Pre-activation and gating pathway of AMPA receptors revealed by full and partial agonists"

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 deposited here contains MD simulation data for GluA2-y2NOW-Open, GluA2-y2FW-Open, GluA2-y2IW-Open, GluA2-y2Glu-Open, GluA2-y2NOW-PreActive and GluA2-y2KA-PreActive systems. All prodcution trajectory (.nc) files were saved at 400 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 GluA2-y2NOW-Open 2251 900 ns AMPAR_Y2_NOW_open_HMR.prmtop AMPAR_Y2_NOW_open_traj_prod_all.nc GluA2-y2FW-Open 2400 960 ns AMPAR_Y2_FW_open_HMR.prmtop AMPAR_Y2_FW_open_traj_prod_all.nc GluA2-y2IW-Open 2400 960 ns AMPAR_Y2_IW_open_HMR.prmtop AMPAR_Y2_IW_open_traj_prod_all.nc GluA2-y2Glu-Open 1250 500 ns AMPAR_Y2_GLU_open_HMR.prmtop AMPAR_Y2_GLU_open_traj_prod_all.nc GluA2-y2NOW-PreActive 2401 960 ns AMPAR_Y2_NOW_preactive_HMR.prmtop AMPAR_Y2_NOW_preactive_traj_prod_all.nc GluA2-y2KA-PreActive 2400 960 ns AMPAR_Y2_KA_preactive_HMR.prmtop AMPAR_Y2_KA_preactive_traj_prod_all.nc The initial structures for the trajectories, along with their corresponding topology files, are provided. The topology files use the .prmtop format, and the coordinate files use the .inpcrd 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.