Protocol for generating MPro trajectories from explicit solvent MD simulations using AMBER22 for the following states: monomer (bound), dimer (half bound, fully bound)

Divided into the following stages: parm: Includes scripts to parametrize non-covalent inhibitors as well as covalently bound inhibitors (custom aa) prep: ff19SB (protein), OPC (water), GAFF (small molecule, if applicable) 0.150M NaCl based on box volume Geenration of topology and coordinate files prod: minimization heating equilibration production

File structure con