How to Calculate RMSD Between Docked and Crystal Poses (Free Tools)

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

Calculate RMSD between docked and crystal ligand poses correctly: obrms, PyMOL and RDKit workflows, symmetry and superposition choices, and the 2 A rule.

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

Key References

• O\u2019Boyle NM et al. Open Babel: an open chemical toolbox. J Cheminform. 2011;3:33. doi:10.1186/1758-2946-3-33
• Morris GM et al. AutoDock4 and AutoDockTools4. J Comput Chem. 2009;30:2785-2791. doi:10.1002/jcc.21256
• RDKit documentation: rdMolAlign module, rdkit.org.

Scope & Limitations

RMSD certifies pose reproduction, not binding affinity; a valid redock says nothing about score accuracy