John D. Chodera john.chodera@choderalab.org

• diamond-structures/ - structures of SARS-CoV-2 main viral protease from DiamondMX/XChem
• receptors/ - prepared receptor structures (in OpenEye .oeb.gz format as well as PDB) with prepared fragments
• molecules/ - input molecule sets for docking
• scripts/ - scripts for preparing receptors and docking and scoring ligands
• docking/ - docked structures (and scores) for use in free energy calculations
• simulation_prep/ - scripts used in preparing gromacs expanded ensemble free energy calculations for Folding@home