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ADT can prepare input for Vina, but Vina itself must be downloaded separately from the Vina GitHub releases . Place vina.exe (Windows) or vina (Linux/macOS) in a folder included in your system PATH.

Proteins downloaded from the Protein Data Bank (PDB) are rarely ready for docking immediately. They contain water molecules, co-crystallized ligands, and often lack hydrogen atoms. download autodock tools work