AutoDock Vina

AutoDock Vina webserver overview

AutoDock Vina is an open-source molecular docking engine for predicting protein-small-molecule binding poses. ProteinIQ runs AutoDock Vina 1.2.7 with Vina, Vinardo, or AutoDock4 scoring and returns ranked poses, affinity estimates, RMSD bounds, preparation records, and downloadable files.

The webserver supports single-ligand docking, independent batch docking, simultaneous ligand docking, selected flexible receptor residues, hydrated ligand workflows, zinc metalloprotein workflows, and score, local, or randomize operations. The AutoDock Vina online guide covers structure preparation, pocket selection, validation, and worked examples.

Pricing

AutoDock Vina jobs start at 15 credits. A standard single-ligand docking run starts at 20 credits. ProteinIQ calculates the exact price from the submitted structures and settings before submission.

Single-ligand docking

Ligand heavy atoms	Exhaustiveness 8	Exhaustiveness 32	Exhaustiveness 64
Up to 30	20 credits	40 credits	57 credits
60	26 credits	51 credits	73 credits
100	31 credits	61 credits	87 credits
150	36 credits	71 credits	100 credits

Batch docking

Ligands	Exhaustiveness 8	Exhaustiveness 32	Exhaustiveness 64
2	28 credits	56 credits	80 credits
3	36 credits	72 credits	102 credits
5	52 credits	104 credits	148 credits
10	92 credits	184 credits	261 credits

Simultaneous co-docking

Ligands	Exhaustiveness 8	Exhaustiveness 32	Exhaustiveness 64
2	40 credits	80 credits	114 credits
3	100 credits	200 credits	283 credits
4	240 credits	480 credits	679 credits
5	500 credits	1,000 credits	1,415 credits

These baseline prices assume Dock, a compact search box, a receptor with up to 4,000 protein atoms, and ligands with no more than 7 rotatable bonds. Batch and simultaneous prices assume up to 30 heavy atoms per ligand. Larger search boxes, receptors, or more flexible ligands increase the exact quote.

Score only, Local only, and Randomize only start at 15 credits. The scoring function and number of returned poses do not currently change the estimate.

Inputs

One receptor and at least one ligand are required. The selected ligand mode determines whether one ligand is docked, several ligands are docked independently, or several ligands are placed in the same pocket.

Input	Accepted formats	Limits and behavior
Receptor	.pdb, .ent, .cif, .mmcif, prepared .pdbqt, or an RCSB PDB ID	Maximum 50 MB. Prepared PDBQT receptors are used as submitted. Other structures follow the selected receptor preparation method.
Ligand	SMILES, .pdbqt, .sdf, .mol, .mol2, .smiles, .smi, .txt, or .csv; PubChem identifiers are also accepted	Maximum 50 MB. Hosted docking supports up to 32 rotatable bonds per ligand.
Job name	Text	Optional label for the run.

Settings

Defaults and ranges follow the ProteinIQ AutoDock Vina tool definition. Dependent controls appear when their parent mode is selected.

The form shows the docking, pocket, and main receptor preparation controls. Advanced settings includes Residues to remove, Residue template assignments, Default alternate location, and Residue alternate locations, alongside Docking operation, Flexible residues, Random seed, Hydrated ligand workflow, and Zinc metalloprotein mode. The remaining Meeko receptor options, the ligand preparation settings, the search and output controls, and custom scoring weights are set through the API, MCP, or workflows.

Docking and pocket

Parameter	Type	Default	Description
Ligand mode	enum	Single ligand	Single ligand, Simultaneous co-docking with up to 5 ligands, or Batch docking with up to 10 ligands.
Scoring function	enum	Vina	Vina, Vinardo, or AutoDock4. Zinc and hydrated workflows require AutoDock4.
Exhaustiveness	integer	8	Search thoroughness, 1 to 64.
Number of poses	integer	9	Maximum poses, 1 to 50.
Pocket definition	enum	Automatic	Automatic uses a detected bound ligand or falls back to the whole receptor. Strict Bound ligand only, Select residues, Manual coordinates, and Whole protein choices are also available.
Bound ligand residues	string	optional	Comma-separated chain:residue IDs. Defines the pocket, then removes those residues.
Binding-site residues	string	conditional	Comma-separated chain:residue IDs. Required for Select residues; residues remain in the receptor.
Pocket padding (A)	number	5	Padding on each side of a ligand or residue pocket, 0 to 20 in 0.5 steps.
Center X (A)	number	0	Manual box center on the X axis.
Center Y (A)	number	0	Manual box center on the Y axis.
Center Z (A)	number	0	Manual box center on the Z axis.
Size X (A)	number	25	Manual box size on the X axis, minimum 1.
Size Y (A)	number	25	Manual box size on the Y axis, minimum 1.
Size Z (A)	number	25	Manual box size on the Z axis, minimum 1.
Whole-protein padding (A)	number	4	Padding around receptor bounds, 0 to 20 in 0.5 steps.

Receptor preparation and workflow

Automatic runs PDB2PQR when standard protein residues have reconstructable missing atoms, including structures with linked or modified residues. Bond records must reference existing, unambiguous atoms. Preparation checks for lost heavy atoms or changed residue identities before Meeko assigns docking charges and atom types. PDB2PQR may adjust atom positions during its native repair; the preparation report records those changes. Unresolved alternate conformers, duplicate atom identities, insufficient reconstruction coordinates, or missing atoms above PDB2PQR's 10% repair limit prevent automatic repair. Choose Always PDB2PQR to request preparation even when no missing atoms are detected.

Automatic uses direct Meeko when no supported missing-atom repair is needed. Direct Meeko retains deposited waters unless they are explicitly selected in Residues to remove. Automatic PDB2PQR repair removes waters; the Retain waters during PDB2PQR switch applies to explicitly selected PDB2PQR preparation. Prepared receptor PDBQT files bypass these preparation steps and retain their submitted charges and atom types.

Waters, cofactors, bound ligands, and alternate conformers need to match the intended receptor model. Component warnings invite review and do not reject a structure merely because it contains nonstandard residues. Meeko makes the final chemistry check. For example, an unexpected inter-residue bond involving HOH A:791 requires inspection of that water and its nearby atoms. Adding A:791 to Residues to remove is appropriate only when that water should be excluded. Preparation does not retry by deleting a failing component or changing chemistry automatically.

Missing binding-site selections and inputs beyond PDB2PQR's supported reconstruction limits are rejected before submission when those conditions can be determined from the selected inputs. A receptor that needs explicit component removal or conformer selection is checked by the native preparer after those choices are applied. Large search boxes produce a warning rather than an arbitrary size restriction.

Parameter	Type	Default	Description
Docking operation	enum	Dock	Dock, Score only, Local only, or Randomize only.
Receptor preparation method	enum	Automatic	Automatic, Direct Meeko, or Always PDB2PQR. Prepared PDBQT is unchanged.
Use PROPKA protonation	boolean	false	Runs PROPKA during Always PDB2PQR preparation.
Receptor pH	number	7	PROPKA pH, 0 to 14 in 0.1 steps.
Retain waters during PDB2PQR	boolean	false	Keeps compatible deposited waters during PDB2PQR preparation only.
Remove detected ligand-like chains	boolean	true	Removes detected ligand-like chains and stale linked records.
Residues to remove	string	optional	Meeko deletion specification for waters, ligands, ions, or other components.
Residue template assignments	string	optional	Meeko assignments in chain:residue=template form.
Default alternate location	string	optional	Alternate-location ID applied to residues with multiple conformers.
Residue alternate locations	string	optional	Residue-specific choices, for example A:42=B,B:17=A.
Blunt polymer ends	string	optional	Meeko polymer-end termination specification.
Delete residues Meeko cannot parameterize	boolean	false	Deletes incomplete or unsupported residues and records their IDs.
Rotatable terminal groups	string	optional	Residues in chain:residue form whose terminal functional group rotates.
Receptor charge model	enum	Gasteiger	Gasteiger or Zero partial charges from Meeko.
Flexible residues	string	optional	Side chains in chain:residue form.
Random seed	integer	0	Nonzero values make identical runs reproducible.
Hydrated ligand workflow	boolean	false	Includes ligand-associated waters. Requires one ligand, Dock, and AutoDock4.
Zinc metalloprotein mode	boolean	false	Enables zinc-specific parameters. Requires AutoDock4.

Ligand preparation

SDF, MOL, and MOL2 ligands are read the way Meeko's mk_prepare_ligand reads them, so submitted hydrogens and their coordinates are kept. If a file leaves hydrogens implicit, ProteinIQ adds them with RDKit and reports how many it added. SMILES ligands get hydrogens and a 3D conformer from RDKit. These settings pass Meeko's ligand options and do not apply to prepared PDBQT ligands, which are used as submitted.

Parameter	Type	Default	Description
Ligand charge model	enum	Gasteiger	Gasteiger, Zero, or Read from file for charges stored in an SDF or MOL2 ligand.
Keep macrocycles rigid	boolean	false	Keeps macrocycles in their input conformation instead of opening them.
Minimum macrocycle size to open	integer	7	Smallest ring, in atoms, that Meeko may open for flexible macrocycle docking.
Double bond penalty	integer	50	Values above 100 prevent opening macrocycles at double bonds.
Allow macrocycle breaks at aromatic carbons	boolean	false	Lets Meeko break bonds to aromatic carbon, retyping those atoms as C.
Keep chorded rings	boolean	false	Returns every ring from exhaustive ring perception.
Keep equivalent rings	boolean	false	Keeps rings with the same size and neighbors.
Flexible amide bonds	boolean	false	Lets amide bonds rotate and become non-planar. Meeko advises against it.
Rigidified bonds	string	optional	One bond per line: a SMARTS pattern and two 1-based atom indices, such as [CX4][OX2] 1 2.
Merged atom types	string	H	Atom types merged into their heavy atoms. Leave empty to keep every hydrogen.

Search and output controls

Parameter	Type	Default	Description
Energy range (kcal/mol)	number	3.0	Retains poses within 0.1 to 20 kcal/mol of the best pose.
Min RMSD between poses (A)	number	1.0	Minimum pose separation, 0.1 to 5.
Max evaluations	integer	0	Scoring-evaluation limit, up to 2147483647. 0 uses Vina's heuristic.
Grid spacing (A)	number	0.375	Affinity-map spacing, 0.1 to 1 in 0.025 steps.
Force even voxels	boolean	false	Requests even affinity-map voxel counts for Vina or Vinardo.
Set unbound ligand energy	boolean	false	Enables a supplied unbound energy in Score only mode.
Unbound ligand energy (kcal/mol)	number	0	Unbound ligand energy used when enabled.
Local optimization max steps	integer	0	Step limit in Local only, up to 2147483647. 0 uses Vina's heuristic.
Randomization max steps	integer	10000	Clash-avoidance step limit in Randomize only, 0 to 100000.
Disable post-docking refinement	boolean	false	Skips final local optimization for Vina or Vinardo.
Use custom scoring weights (advanced)	boolean	false	Enables weights for the selected scoring function.

Custom scoring weights

These fields are available when Use custom scoring weights (advanced) is enabled. The defaults are the tool's current Vina, Vinardo, and AutoDock4 values.

Parameter	Type	Default	Description
Vina gauss1	number	-0.035579	Vina weight.
Vina gauss2	number	-0.005156	Vina weight.
Vina repulsion	number	0.840245	Vina weight.
Vina hydrophobic	number	-0.035069	Vina weight.
Vina hydrogen	number	-0.587439	Vina weight.
Vina glue	number	50	Vina weight.
Vina rotation	number	0.05846	Vina weight.
Vinardo gauss1	number	-0.045	Vinardo weight.
Vinardo repulsion	number	0.8	Vinardo weight.
Vinardo hydrophobic	number	-0.035	Vinardo weight.
Vinardo hydrogen	number	-0.6	Vinardo weight.
Vinardo glue	number	50	Vinardo weight.
Vinardo rotation	number	0.05846	Vinardo weight.
AD4 van der Waals	number	0.1662	AutoDock4 weight.
AD4 hydrogen bond	number	0.1209	AutoDock4 weight.
AD4 electrostatic	number	0.1406	AutoDock4 weight.
AD4 desolvation	number	0.1322	AutoDock4 weight.
AutoDock4 glue	number	50	AutoDock4 weight.
AutoDock4 rotation	number	0.2983	AutoDock4 weight.

Outputs

Output	What it contains
Structure	Interactive receptor and ligand poses for inspecting binding geometry.
Data	Docking affinity, RMSD lower and upper bounds, and native energy terms. Score only and Local only also return the named energy-term vector.
Files	Individual pose PDBQT files, a combined native PDBQT, prepared receptor and ligand files, the prepared flexible residues when side chains or terminal groups are flexible, optional PDB2PQR output, and preparation metadata. Hydrated workflows include their additional water-containing files.
Logs	The curated run.log with preparation, resolved automatic-pocket decisions, box, docking, and output details.

Understanding docking results

AutoDock Vina scores are approximate model outputs. Within a run that uses the same receptor preparation, ligand representation, box, scoring function, and settings, more negative affinity values rank as more favorable. Scores from different scoring functions or differently prepared systems are not directly comparable.

Result	Interpretation
Affinity	Predicted binding score in kcal/mol. It is useful for within-protocol ranking, not as a measured binding constant.
RMSD lower and upper bounds	Distance from the best returned pose cluster. They describe pose similarity, not experimental accuracy.
Energy terms	Components of the selected scoring model. AutoDock4 includes map-based electrostatic and desolvation terms; Vina and Vinardo use different empirical terms.
Pose geometry	Contacts, clashes, ligand strain, protonation, alternate locations, waters, and box placement still require structural inspection.