Unveiling the Catalytic Mechanism of NADP+-Dependent Isocitrate Dehydrogenase with QM/MM Calculations

Raw molecular dynamics simulations for the complexes simulated for 20 ns with the AMBER 12 software. Details can be found in the original manuscript (https://doi.org/10.1021/acscatal.5b01928). Molecular topology in AMBER Parameter Topology format and Trajectories in NETCDF binary coordinate format. Two protonation states were simulated: non-charged state of catalytic Lys212/Asp275 (LYN626+ASH275+ASP666) and charged state of catalytic Lys212/Asp275 (LYS626+ASP275+ASP666) Production trajectories are included in the MM-MD folders. Input and restart coordinates files for reproducibility are located in folders inputs and rst. Instructions for the calculations are summarized in amber_min-md.sh.