AutoDock Container

Tools included in the container are MGL Tools and AutoDock Vina. Two versions are available: nvidia and mesa-supported container. For nvidia support, you need to install NVIDIA driver on host and install nvidia-docker2.

To download:

1. docker pull afandiadib/autodock:nvidia
2. docker pull afandiadib/autodock:mesa

Example of usage:

AutoDock Tools - mesa

To run autodock tools:

docker run --rm --user=$(id -u) \
           --workdir=`pwd` \
           --env=DISPLAY \
           --volume=/home/$USER:/home/$USER \
           --volume=/media:/media \
           --volume=/mnt:/mnt \
           --volume=/etc/group:/etc/group:ro \
           --volume=/etc/passwd:/etc/passwd:ro \
           --volume=/etc/shadow:/etc/shadow:ro \
           --volume=/etc/sudoers.d:/etc/sudoers.d:ro \
           --volume=/tmp/.X11-unix:/tmp/.X11-unix:rw \
           --volume=/usr/share/icons:/usr/share/icons \
           --device=/dev/dri \
           afandiadib/autodock:nouveau adt

If permission denied, you need to change ownership of /dev/dri on host for gpu acceleration.

sudo chown -R $USER /dev/dri

AutoDock Tools - nvidia

To run autodock tools:

docker run --rm --user=$(id -u) \
           --workdir=`pwd` \
           --env=DISPLAY  \
           --volume=/home/$USER:/home/$USER \
           --volume=/media:/media \
           --volume=/mnt:/mnt \
           --volume=/etc/group:/etc/group:ro \
           --volume=/etc/passwd:/etc/passwd:ro \
           --volume=/etc/shadow:/etc/shadow:ro \
           --volume=/etc/sudoers.d:/etc/sudoers.d:ro \
           --volume=/tmp/.X11-unix:/tmp/.X11-unix:rw \
           --volume=/usr/share/icons:/usr/share/icons \
           --runtime=nvidia \
           afandiadib/autodock:nvidia adt

Autodock Vina - mesa

docker run --rm \
           --workdir=`pwd` \
           --volume=`pwd`:\`pwd\` \
           afandiadib/autodock:nouveau vina

Tip

To run vina, alias the docker command in .bashrc for convenience:

alias vina='docker run --rm --workdir=`pwd` --volume=`pwd`:`pwd` afandiadib/autodock:nouveau vina'

For virtual screening, it is better to run interactively though.