Docking Returns No Poses: 9 Reasons and Fixes

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

Vina finished but the output file has zero poses? The 9 causes — box clipping, bad ligand chemistry, tight energy range, unwritten outputs — with diagnostics and exact fixes.

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

Key References

• Trott O, Olson AJ. AutoDock Vina: improving the speed and accuracy of docking. J Comput Chem. 2010;31(2):455-461. doi:10.1002/jcc.21334
• Kim S et al. PubChem in 2021: new data content and improving web interfaces. Nucleic Acids Res. 2021;49(D1):D1388-D1395. doi:10.1093/nar/gkaa971
• AutoDock Vina 1.2.x user guide output documentation, Scripps Research Institute.

Scope & Limitations

Some batch wrappers swallow Vina warnings; reproduce failing cases with plain command-line Vina before concluding