MolDraw › Chemistry tools › AutoDock Vina Grid Box Calculator
AutoDock Vina Grid Box Calculator
In short: Get center_x/y/z and size_x/y/z for the Vina search box from a co-crystallised ligand, a list of binding-site residues or a centre you type. Download a ready config.txt. It is free and runs in your browser.
config.txt settings
Search box
config.txt
Box over the structure
2D projections: grey = protein atoms near the box, pink = selected ligand, teal = box.
How the box is calculated
size = (max − min of selected atoms) + 2 × padding center = (max + min) / 2
The tool takes the heavy atoms of the chosen ligand or residues, finds their smallest and largest x, y and z, and adds the padding on both sides of each axis. With the centroid option the centre is the mean atom position, and each edge is widened so the box still covers every atom. Vina reads size_x as the full edge length in ångströms.
Worked example: 1A28 (progesterone receptor)
The 23 heavy atoms of progesterone (STR A 1) span x 21.009–24.697, y 7.301–12.976 and z 55.052–65.512 Å. The middle is (22.853, 10.139, 60.282). With 5 Å padding the box is 13.688 × 15.675 × 20.460 Å, a volume of 4,390 ų. The radius of gyration is 3.66 Å, so the eBoxSize suggestion is 10.5 Å per edge.
Choosing the size
- Padding 4–6 Å per side is typical for redocking a ligand of similar size. Use 8 Å or more for a larger ligand than the crystal one.
- 30 Å limit. Vina was tuned on boxes up to about 30 × 30 × 30 Å and prints a warning when the volume exceeds 27,000 ų. Larger boxes need higher exhaustiveness.
- eBoxSize. Feinstein & Brylinski (J. Cheminform. 2015, 7, 18) found the best docking accuracy with a cubic edge of 2.857 × the ligand’s radius of gyration.
- AutoDock4 / AutoGrid use grid points instead: npts = size / spacing (0.375 Å), rounded up to an even number. The table shows these values.
How to set up a Vina run
- Load the original PDB with the ligand still in it, or import it by PDB ID.
- Pick the ligand, or switch to residues if there is no ligand. Keep padding at about 5 Å.
- Check the warnings and the projections: the box should cover the pocket, not the whole protein.
- Set the receptor and ligand file names. Prepare those files with the PDB cleaner, protonation at pH and the PDB to PDBQT converter.
- Download
config.txtand runvina --config config.txt. Redock the crystal ligand first: an RMSD under 2 Å means the box and settings work.
Limitations
- The box is axis-aligned, as in Vina. It is not rotated to fit an elongated pocket.
- Residue mode uses all atoms of those residues, including side chains that point away from the pocket. Pick lining residues, or add a little less padding.
- It does not find pockets. If there is no ligand and you do not know the site, use a pocket-finding tool first.
- Altlocs: only altloc A (or blank) atoms are used.
- The 3D preview needs WebGL2 and shows at most 900 atoms near the box.
Frequently asked questions
How do I find center_x, center_y and center_z for Vina?
Take the co-crystallised ligand in the PDB file and use the middle of its bounding box (or its centroid). For 1A28 progesterone the bounding-box middle is (22.853, 10.139, 60.282). Without a ligand, use the binding-site residues instead.
How big should the Vina box be?
Large enough for the ligand to move and rotate: the ligand size plus about 5 Å on each side is a common choice. Feinstein and Brylinski (2015) found the best accuracy with an edge of about 2.857 times the ligand's radius of gyration. Vina warns when the volume passes 27,000 ų (30 × 30 × 30 Å).
Is size_x the full width or half the width?
The full width in ångströms. The box runs from center_x − size_x/2 to center_x + size_x/2. AutoDock4 instead uses a number of grid points (npts) times the spacing, which the tool also shows.
What exhaustiveness should I use?
The default is 8. Raise it (16–32) for larger boxes, flexible ligands or final runs. Run time grows roughly in proportion to exhaustiveness.
Can I use this for blind docking?
You can enter a manual box around the whole protein, but Vina is tuned for boxes up to about 30 Å. For blind docking split the surface into several boxes, or find pockets first with a pocket-detection tool.
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