The qfvina.x application, described in the first component above, accepts several command-line arguments, including --dockingType, which can be set to qfvina for the new QFVina or QFVinardo methods, or vina for traditional flexible ligand docking. The --scoringFunction argument accepts either vina or vinardo options. The --protein argument specifies the target PDB file, and an optional --ligand argument can define the ligand SDF file. If not specified, the scheme to perform all docking automatically handles it internally. The --dockedLigand from the downloaded PDB structure is used only to define the center of the docking box as the geometric center of the docked ligand. If not specified, the --centerX, --centerY, and --centerZ arguments must be used to specify the center of the docking box. In this article, we used the docked ligands from the original PDB file to define the docking box center. There is also a --boxsize argument that defines a cubic docking box, and we may introduce separate inputs for X, Y, and Z directions in the next version. For all docking calculations in this work, we used a 20 Å × 20 Å × 20 Å cubic docking box.