"Ligand Outside the Grid Box": Grid Errors and the Fix

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

Fix the Vina ligand outside the grid box error: box center and size vs ligand extent, the padding rule, blind-docking values, and a worked example with exact numbers.

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
• Cosconatti S et al. Virtual screening with AutoDock: theory and practice. Expert Opin Drug Discov. 2010;5(6):591-607.
• Seeliger D, de Groot BL. Ligand docks and proteins: a receptor-centric perspective. J Comput Aided Mol Des. 2010;24(5):417-422.

Scope & Limitations

Larger boxes linearly increase compute cost; oversized boxes also dilute search density and can lower pose quality