Vina box generator

Why the box matters

AutoDock Vina searches for ligand poses only inside a rectangular box that you define with a centre (center_x/y/z) and edge lengths (size_x/y/z) in ångström. Getting the box wrong is one of the most common reasons redocking fails. If the box is too small, the correct pose physically does not fit. If it is too large, the search becomes inefficient, the number of local minima grows, and you need much higher exhaustiveness to find the same answer. If it is centred in the wrong place, Vina finds a "pose" on the protein surface with a perfectly respectable-looking score. This tool takes the guesswork out by computing the box from atoms you choose, and it writes the configuration in the formats Vina actually reads.

How the box is computed

• Selection. Pick the atoms that define the site. Usually this is the co-crystallised ligand (by its three-character residue name, such as MK1), or a set of binding-site residues from the literature. Chain, residue number, ranges and residue names are supported. Only the first MODEL of a multi-model file is read, and only blank or "A" alternate locations are kept, so alternative conformations are not counted twice.
• Extent mode (default). The box is the axis-aligned bounding box of the selected atoms, enlarged by the padding on each side. 4–6 Å is typical when you define the box from a bound ligand, to leave room for rotation and for ligands larger than the reference.
• Rg mode. A cubic box with edge 2.857 × R_g of the selected atoms. This follows Feinstein & Brylinski (2015), who found that docking accuracy with Vina peaks when the box edge is about 2.9 times the ligand's radius of gyration. Use it when the selection is the ligand you are about to dock, or a similar one.
• Centre: either the middle of the bounding box (recommended, because it keeps the padding symmetric) or the plain average of the atom coordinates.

The tool warns if the search volume is above 27,000 ų (30 × 30 × 30 Å), where Vina itself prints a warning and the search becomes much less reliable. It also warns if any edge is shorter than 10 Å, which is unlikely to fit a drug-sized ligand.

Worked example: HIV-1 protease with indinavir (PDB 1HSG)

Click Load example to load a trimmed 1HSG file containing the catalytic-site residues 25, 50 and 82 of both chains and the bound inhibitor MK1. With the selection MK1, padding 5 Å and bounding-box centring:

• 45 ligand heavy atoms selected. Extent 14.854 × 10.214 × 8.635 Å.
• Centre (11.634, 22.470, 5.859). Size 24.854 × 20.214 × 18.635 Å. Volume ≈ 9,362 ų.
• In Rg mode, R_g = 5.638 Å gives a 16.107 Å cube (≈ 4,179 ų).

Selecting the residues instead (A:25,B:25,A:50,B:50,A:82,B:82) moves the centre by about 2 Å and enlarges the box, because flap residue 50 sits above the ligand. Both are reasonable boxes. The ligand-based one is tighter. The Vina + Meeko tutorial uses this box to redock indinavir and checks the RMSD of the result.

Assumptions and limitations

• Coordinates must be in the same frame as the receptor PDBQT you dock into. If you superimposed, protonated or minimised the structure in another program, recompute the box from that file.
• The box is axis-aligned, as Vina requires. Long, diagonal grooves therefore need a larger box than their length suggests.
• PDB fixed-column format is assumed (the official wwPDB format). Some programs write non-standard column layouts. If the atom count looks wrong, check the file. mmCIF is not supported yet: convert it with Open Babel, PyMOL or gemmi convert.
• Blind docking (a box around the whole protein) is possible, but it is a different experiment. It needs much higher exhaustiveness, and the results should be read with care.
• The box does not replace receptor preparation. Missing side chains, protonation states, waters and cofactors all change docking results far more than a 1 Å shift of the box.

References

1. Eberhardt J, Santos-Martins D, Tillack AF, Forli S. AutoDock Vina 1.2.0: new docking methods, expanded force field, and Python bindings. J Chem Inf Model 2021;61:3891–3898. doi:10.1021/acs.jcim.1c00203
2. Trott O, Olson AJ. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem 2010;31:455–461. doi:10.1002/jcc.21334
3. Feinstein WP, Brylinski M. Calculating an optimal box size for ligand docking and virtual screening against experimental and predicted binding pockets. J Cheminform 2015;7:18. doi:10.1186/s13321-015-0067-5
4. AutoDock Vina documentation, "Basic docking" and configuration file reference. autodock-vina.readthedocs.io
5. Chen Z, Li Y, Chen E, et al. Crystal structure at 1.9-Å resolution of human immunodeficiency virus (HIV) II protease complexed with L-735,524, an orally bioavailable inhibitor of the HIV proteases. J Biol Chem 1994;269:26344–26348. PDB entry 1HSG.

Results are for research and education and are not a substitute for checking against the primary literature. See the disclaimer. Found a bug? Report it.