there is a paper that shows all you want and gives the pipeline for this. read it and you will give all you want.

"Targeting D-Ribose-Binding Proteins in Brucella melitensis: A Novel Frontier Against Antibiotic Resistance"

doi: https://doi.org/10.1101/2025.02.28.640864

• Prepare ligands (SDF → PDBQT) and proteins (PDB → PDBQT) externally with Chimera/AutoDock Tools for accuracy, then import into PyRx. Although, you can import ligands directly using OpenBible available by default in PyRx. And you can import all ligands at once as an SDF file for efficiency; no accuracy loss.
• Use AutoDock Tools for complex protein prep; PDBQT is required for docking.
• Streamline multiple ligand docking with Multipack Screening, organizing ligands by class and documenting grid settings.
• Prioritize binding affinity and key interactions in analysis; use entropy metric to identify correlated docking metrics for antidiabetic targets.