SDF vs MOL2 vs PDBQT vs PDB: Which File Format When?

By BioDockify Computational Research Team · September 27, 2026 · Reference

SDF vs MOL2 vs PDBQT vs PDB compared — what each stores (coordinates, charges, bond orders, torsions), why AutoDock needs PDBQT, free conversion, and format errors to avoid.

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

Key References

• Open Babel documentation — format conversion guide.
• AutoDock/Vina preparation documentation (PDBQT specification).

Scope & Limitations

Tool-specific quirks exist beyond the core formats