# Autodock Vina 1.2.5


{{< admonition success "Installed" true >}}
This software should be available with no extra configuration.
{{< /admonition >}}

## AutoDock Vina: Docking and virtual screening program

**AutoDock Vina** is one of the **fastest** and **most widely used**
**open-source** docking engines. It is a turnkey computational docking program
that is based on a simple scoring function and rapid gradient-optimization
conformational search. It was originally designed and implemented by Dr. Oleg
Trott in the Molecular Graphics Lab, and it is now being maintained and
develop by the Forli Lab at The Scripps Research Institute.

* AutoDock4.2 and Vina scoring functions
* Support of simultaneous docking of multiple ligands and batch mode for
  virtual screening
* Support of macrocycle molecules
* Hydrated docking protocol
* Can write and load external AutoDock maps
* Python bindings for Python 3 (Linux and Mac)

AutoDock Vina is distributed under the Apache License, Version 2.0.

## Documentation

The installation instructions, documentation and tutorials can be found on [readthedocs.org](https://autodock-vina.readthedocs.io/en/latest/).

## Citations

* [J. Eberhardt, D. Santos-Martins, A. F. Tillack, and S. Forli. (2021).
   AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python
   Bindings. Journal of Chemical Information and Modeling.](https://pubs.acs.org/doi/10.1021/acs.jcim.1c00203)
* [O. Trott and A. J. Olson. (2010). AutoDock Vina: improving the speed and
   accuracy of docking with a new scoring function, efficient optimization, and
   multithreading. Journal of computational chemistry, 31(2),
   455-461.](https://onlinelibrary.wiley.com/doi/10.1002/jcc.21334)

-------------------------------------------------------------------------------

## Location and version

```console
$ which vina
/local/cluster/bin/vina
$ vina --version
AutoDock Vina 616d6c8-mod
```

## help message

```console
$ vina --help
AutoDock Vina 616d6c8-mod

Input:
  --receptor arg             rigid part of the receptor (PDBQT)
  --flex arg                 flexible side chains, if any (PDBQT)
  --ligand arg               ligand (PDBQT)
  --batch arg                batch ligand (PDBQT)
  --scoring arg (=vina)      scoring function (ad4, vina or vinardo)

Search space (required):
  --maps arg                 affinity maps for the autodock4.2 (ad4) or vina
                             scoring function
  --center_x arg             X coordinate of the center (Angstrom)
  --center_y arg             Y coordinate of the center (Angstrom)
  --center_z arg             Z coordinate of the center (Angstrom)
  --size_x arg               size in the X dimension (Angstrom)
  --size_y arg               size in the Y dimension (Angstrom)
  --size_z arg               size in the Z dimension (Angstrom)
  --autobox                  set maps dimensions based on input ligand(s) (for
                             --score_only and --local_only)

Output (optional):
  --out arg                  output models (PDBQT), the default is chosen based
                             on the ligand file name
  --dir arg                  output directory for batch mode
  --write_maps arg           output filename (directory + prefix name) for
                             maps. Option --force_even_voxels may be needed to
                             comply with .map format

Misc (optional):
  --cpu arg (=0)             the number of CPUs to use (the default is to try
                             to detect the number of CPUs or, failing that, use
                             1)
  --seed arg (=0)            explicit random seed
  --exhaustiveness arg (=8)  exhaustiveness of the global search (roughly
                             proportional to time): 1+
  --max_evals arg (=0)       number of evaluations in each MC run (if zero,
                             which is the default, the number of MC steps is
                             based on heuristics)
  --num_modes arg (=9)       maximum number of binding modes to generate
  --min_rmsd arg (=1)        minimum RMSD between output poses
  --energy_range arg (=3)    maximum energy difference between the best binding
                             mode and the worst one displayed (kcal/mol)
  --spacing arg (=0.375)     grid spacing (Angstrom)
  --verbosity arg (=1)       verbosity (0=no output, 1=normal, 2=verbose)

Configuration file (optional):
  --config arg               the above options can be put here

Information (optional):
  --help                     display usage summary
  --help_advanced            display usage summary with advanced options
  --version                  display program version
```

software ref: <https://github.com/ccsb-scripps/AutoDock-Vina>  
research ref: <https://pubs.acs.org/doi/10.1021/acs.jcim.1c00203>