PDBQT to PDB: Why Hydrogens Are Missing and How to Restore Them

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

Convert PDBQT poses to PDB: why hydrogens vanish, the obabel command restoring them at pH 7.4, what the round-trip loses, and fixes for viewer and MD problems.

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",
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Scope & Limitations

Re-added hydrogens are geometry-idealized, not optimized against the receptor; for publication-quality H-bond analysis, minimize the complex first