How to Convert PDB to PDBQT: Open Babel and the -xr Flag

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

Convert PDB to PDBQT with Open Babel: ligand vs receptor commands, the -xr rigid-receptor flag, what charges and torsion trees are added, and mistakes that break runs.

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

Open Babel Gasteiger charges differ slightly from AutoDockTools.amber99 charges; scores shift by a few tenths of a kcal/mol between tools