Free Vina search-space helper · Dock tools
AutoDock Vina Grid Box Calculator
Upload a reference ligand to compute Center X/Y/Z and Size — copy config.txt or open Dock with a custom box.
Drop a reference ligand file here
.pdb (HETATM) or .sdf / .mol · local JS only · never uploaded
Grid box result
Upload a reference ligand above. Center and Size will appear here for your Vina config.txt.
How to calculate an AutoDock Vina grid box online
You do not need PyMOL, ChimeraX, or AutoDockTools just to get center_x / center_y / center_z and box sizes. Upload a reference ligand, tune padding, and copy a Vina-ready config.txt snippet — all in the browser.
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Upload a reference ligand PDB or SDF
Prefer a holo structure: we read non-solvent HETATM (co-crystallized ligand). You can also upload an extracted ligand .sdf/.mol or a ligand-only PDB with ATOM records. Parsing uses the FileReader API only.
- 2
Review Center and tune padding (5–10 Å)
Center is the arithmetic mean of atom X/Y/Z. Size on each axis is the ligand bounding-box span (max − min) plus your padding. If several HETATM groups exist, pick the intended ligand before copying.
- 3
Copy config.txt or start docking
Paste the snippet into a local AutoDock Vina config, or click Copy Coordinates & Start Docking to open our online form with the custom box prefilled.
What is an AutoDock Vina grid box?
AutoDock Vina does not search the entire protein. It samples ligand poses inside a rectangular search space (often called the grid box or docking box) defined by a center point and lengths along X, Y, and Z in Ångströms. Those six numbers — center_x, center_y, center_z and size_x, size_y, size_z — are the most common source of “wrong pocket” or failed redock results in student and methods write-ups.
The standard way to place the box for a holo structure is to center it on the co-crystallized reference ligand (the molecule already bound in the PDB). Averaging that ligand’s atom coordinates gives a reproducible pocket center; extending the ligand’s bounding box by a few Ångströms gives a search volume large enough for analogs without exploding the search space.
This free grid box calculator is built for that long-tail workflow: you already have a ligand PDB or SDF, you need exact Vina coordinates, and you want to dock next — not install AutoDockTools or script Biopython locally. Pair the box with a cleaned receptor from our PDB cleaner and a ligand SMILES from name to SMILES, then run docking on the Dock homepage.
Vina config.txt grid box parameters explained
Local AutoDock Vina reads a plain-text config file. The snippet this tool copies maps 1:1 to the search-space keys below.
| Parameter | Meaning | How we compute it |
|---|---|---|
| center_x / y / z | Geometric center of the search box (Å) | Mean of selected ligand atom coordinates |
| size_x / y / z | Box length along each axis (Å) | Ligand span (max − min) + padding (5–10 Å) |
| receptor / ligand | Paths to PDBQT inputs (local Vina) | Not set here — add in your own config after prep |
| exhaustiveness | Global search thoroughness | Not part of the box; Dock online uses 8 by default |
Example snippet after uploading a reference ligand:
center_x = 12.345 center_y = -3.210 center_z = 18.900 size_x = 22.5 size_y = 20.0 size_z = 18.0
How large should the docking box be?
Oversized boxes raise false positives and slow sampling; undersized boxes clip poses and hurt redock RMSD. Use these starting points, then verify with a native-ligand redock when possible.
| Use case | Suggested padding | Typical box |
|---|---|---|
| Drug-like redock / close analogs | 5–8 Å | ~18–25 Å per side after padding |
| Larger peptidomimetic or flexible ligand | 8–10 Å | Watch size_z if the pocket is deep |
| Coursework / Methods default cube | Often fixed 20×20×20 Å cube | Center on co-crystal ligand; cite PDB + box |
| Apo pocket / no reference ligand | N/A for this tool | Use residue anchors or pocket prediction instead |
For a full prep checklist (receptor cleanup, protonation, redock checks), see preparing receptors and ligands for AutoDock Vina and the AutoDock Vina online tool guide.
When to center the box on a reference ligand
Use this calculator when you have a co-crystallized inhibitor, substrate, or fragment in the binding site and want Vina to search that pocket for the same ligand (redock) or close analogs. Extract the ligand as SDF if your PDB has many heteroatoms, or upload the full holo PDB and select the correct HETATM group.
Do not rely on ligand centering alone for apo structures, allosteric sites far from the co-crystal ligand, or when the crystallographic ligand is a crystal artifact (buffer, detergent) rather than the pharmacologically relevant binder. In those cases use catalytic residue midpoints, published pocket definitions, or Dock’s automatic pocket ranking — then still record the final center_* / size_* in your Methods paragraph.
Before docking analogs, clean waters and unwanted heteroatoms from the receptor with the PDB Cleaner. Keep the reference ligand file separate for this calculator so pocket definition stays independent of the receptor prep file you submit to Vina.
Grid box calculator FAQ
Short answers for students and researchers setting AutoDock Vina search-space coordinates from a reference ligand.
The grid box is the rectangular volume where AutoDock Vina samples ligand poses. It is defined by a center (X, Y, Z in Å) and sizes along each axis. Everything outside that box is ignored during docking, so the center should sit in the intended binding pocket.
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