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Set the number of runs (usually 10 to 50 for initial testing). Export the Docking Parameter File (.dpf) . 4. Troubleshooting Common Issues

Run the installer and choose a simple installation path (e.g., C:\MGLTools1.5.7 ). Avoid paths with spaces, as this can sometimes cause issues with Python scripts. download autodock tools work

Just like the protein, the ligand must be saved in the .pdbqt format via the Ligand > Input > Open menu. Phase C: Setting the Grid Box Set the number of runs (usually 10 to