How to Convert SDF to PDBQT (Single Ligands and Whole Libraries)

By BioDockify Computational Research Team · September 3, 2026 · Tutorials

Convert SDF to PDBQT for docking: single ligands and whole libraries with Open Babel, torsion trees, charge handling, and the validation steps Vina expects.

Read the complete article with tables, code and references on BioDockify.

Key References

• Boyle NM et al. Open Babel: an open chemical toolbox. J Cheminform. 2011;3:33. doi:10.1186/1758-2946-3-33",
• ,

Scope & Limitations

Conversion rules here target AutoDock Vina workflows; AutoDock4 scoring uses PDBQT charges differently