Step-by-Step PyRx Protocol:

1. Load Macromolecule: Navigate to File → Load Molecule → Select receptor.pdb. Right-click the structure in the Navigator and choose Make Macromolecule (PyRx automatically adds polar hydrogens and converts it into PDBQT).
2. Import Ligands: In the OpenBabel tab, import your ligand SDF or multi-molecule SDF file. Click Energy Minimize (using MMFF94 force field with 200 conjugate gradient steps).
3. Convert Ligands to PDBQT: Right-click the minimized ligand list and select Convert to AutoDock Ligand (PDBQT).
4. Configure Vina Wizard: Switch to the Vina Wizard tab → Select your Macromolecule and active Ligands → Click Forward.
5. Set Grid Box Dimensions: Adjust the interactive 3D bounding box cage. Specify center_x, center_y, center_z and size_x, size_y, size_z (standard box size: $20 \times 20 \times 20\text{ \AA}^3$).
6. Run Vina: Set Exhaustiveness = 16 (or 32 for publication benchmarks) → Click Forward to execute multi-threaded parallel docking.
7. Analyze Results: Export the binding affinity table ($\Delta G$ in kcal/mol) and RMSD bounds. Select top poses to inspect 3D interactions in the viewport.

receptor = target.pdbqt
ligand = candidate_01.pdbqt

center_x = -10.45
center_y = 12.30
center_z = 68.20

size_x = 22.0
size_y = 22.0
size_z = 22.0

energy_range = 3.0
exhaustiveness = 32
num_modes = 9
cpu = 8

mkdir -p docking_results

for lig in ligands/*.pdbqt; do
    base=$(basename "$lig" .pdbqt)
    echo "Docking ligand: $base..."
    vina --receptor target.pdbqt \
         --ligand "$lig" \
         --config conf_coords.txt \
         --out "docking_results/${base}_out.pdbqt" \
         --log "docking_results/${base}.log"
done

# Extract top binding affinities across all screening runs
grep "   1 " docking_results/*.log | awk '{print $1, $2, $3}' | sort -k3,3n > ranked_hits.txt
head -n 20 ranked_hits.txt