Installation

Warning

Currently, the python bindings and the binary installation are two separate processes. The installation of the python bindings does not include the Vina executable, and vice versa.

Unix- and Linux-based OS

Vina is expected to work on x86 and compatible 64-bit Linux systems. The executable for the latest release are available here: https://github.com/ccsb-scripps/AutoDock-Vina/releases.

Running:

./vina_1.2.0_linux_x86_64 --help

If the executable is in your PATH, you can just type “vina –help” instead.

macOS

Vina is expected to work on macOS 10.15 (Catalina) and newer. The executable for the latest release are available here: https://github.com/ccsb-scripps/AutoDock-Vina/releases.

Running:

./vina_1.2.0_macos_x86_64 --help

If the executable is in your PATH, you can just type “vina –help” instead.

Python bindings

Currently working on Linux and Mac. We did not test on Windows.

AutoDock Vina installation using pip:

Note

When using pip, it’s good pratice to use a virtual environment and also the easiest solution (see meeko in Software requirements). An example with the Conda package manager is available further down.

$ pip install -U numpy vina

AutoDock Vina installation in a Conda environment:

The Anaconda Python distribution, which can be download from https://docs.continuum.io/anaconda/install. This is a Python distribution specially designed for scientific applications, with many of the most popular scientific packages preinstalled. Alternatively, you can use Miniconda, which includes only Python itself, plus the Conda package manager.

  1. Begin by installing the most recent 64 bit, Python 3.x version of either Anaconda or Miniconda

  2. Create a dedicated environment for AutoDock Vina. This environment can be re-used for installing meeko (see Software requirements):

$ conda create -n vina python=3
$ conda activate vina
$ conda config --env --add channels conda-forge
  1. And type the following command to install NumPy and AutoDock Vina:

$ conda install -c conda-forge numpy swig boost-cpp sphinx sphinx_rtd_theme
$ pip install vina

Building from Source

Warning

Building Vina from source is NOT meant to be done by regular users!

  • Step 1: Install a C++ compiler suite
    • Ubuntu/Debian: sudo apt-get install build-essentials

    • macOS: Install Xcode from the AppStore and the Command Line Tools (CLT) from the terminal xcode-select --install

  • Step 2: Install Boost and SWIG
    • Ubuntu/Debian: sudo apt-get install libboost-all-dev swig

    • macOS (with Homebrew): brew install boost swig

  • Step 3: Build Vina

    Start by downloading the lastest version of AutoDock Vina from github:

    $ git clone https://github.com/ccsb-scripps/AutoDock-Vina
    

    To compile the binary (you might need to customize the Makefile by setting the paths to the Boost library):

    $ cd AutoDock-Vina/build/linux/release
    $ make
    

    To compile the Python bindings:

    Note

    The Conda package manager is used here to easily install the several dependencies needed to build the Autodock-Vina python bindings (see above how to create a dedicated environment).

    $ conda activate vina
    $ cd AutoDock-Vina/build/python
    $ conda install -c conda-forge numpy boost-cpp swig
    $ rm -rf build dist *.egg-info (to clean previous installation)
    $ python setup.py build install