Vina - Python interface to AutoDock Vina

1.2.7 verified Fri May 01 auth: no python

vina provides a Python interface to AutoDock Vina, a widely used tool for molecular docking and virtual screening. Current version: 1.2.7, release cadence: irregular, last update 2023.

pip install vina

Common errors

error ImportError: cannot import name 'Vina' from 'vina' ↓

cause The class was renamed to Vino in vina 1.2.0.

fix

Use from vina import Vino instead.

error RuntimeError: Vina executable not found. Please install AutoDock Vina. ↓

cause The Vina binary is missing from PATH.

fix

Install AutoDock Vina binary (e.g., via conda or download from official site) and ensure it's in PATH.

error ValueError: Invalid file format. Expected .pdbqt. ↓

cause Input files must be in PDBQT format.

fix

Convert your receptor and ligand to PDBQT using tools like prepare_receptor4.py and prepare_ligand4.py from AutoDockTools.

Warnings

gotcha The vina package requires the AutoDock Vina binary installed and accessible in PATH. The Python package is just a wrapper. ↓

fix Install Vina binary (e.g., conda install -c bioconda autodock-vina) before using the Python package.

gotcha Input files (protein, ligand) must be in PDBQT format. Standard PDB or SDF will cause errors. ↓

fix Use tools like Meeko or AutoDockTools to convert ligands to PDBQT.

deprecated The class name changed from 'Vina' to 'Vino' in version 1.2.0. Older tutorials use `from vina import Vina`. ↓

fix Use `from vina import Vino` for version 1.2.x. For compatibility, check `vina.__version__`.

Imports

Vina
```
from vina import Vina
```
Correct import for the main docking class.

Quickstart

Basic molecular docking using Vina Python interface.

from vina import Vino

v = Vino(sf='vina')
v.set_receptor('protein.pdbqt')
v.set_ligand('ligand.pdbqt')
v.compute_vina(center=[0, 0, 0], box_size=[20, 20, 20])
v.write_poses('output.pdbqt', n_poses=5)
print('Docking complete')