AutoDock Vina on Google Colab: Free GPU Docking, Step-by-Step

By BioDockify Computational Research Team · September 19, 2026 · Tutorial

Run AutoDock Vina in Google Colab free: install commands, PDBQT preparation, batch docking loop, GPU notes and when a cloud platform beats a notebook.

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

Key References

• Trott, O. & Olson, A.J. AutoDock Vina. J. Comput. Chem. 31, 455–461 (2010). DOI: 10.1002/jcc.21334
• Eberhardt, J. et al. AutoDock Vina 1.2.0. J. Chem. Inf. Model. 61, 3891–3898 (2021). DOI: 10.1021/acs.jcim.1c00203
• Google Colab FAQ — GPU availability and usage limits. https://research.google.com/colaboratory/faq.html

Scope & Limitations

Colab free tier disconnects idle sessions and caps GPU hours — not for overnight batches Vina 1.2.x scoring is CPU-based; a GPU helps GNINA, not classic Vina Notebook state is ephemeral: mount Drive or results are lost at disconnect