Apptainer/Singularity container usage

The recommended way to use CaverDock is by using the pre-built image for the Apptainer engine. This approach is very effective as it does not require any other installation than the Apptainer engine itself (which might be already available in your HPC environment) and can be used immediately after download. More details about installation can be found in the Installation section.

Note

If you are still using the Singularity engine from Sylabs, just replace apptainer with singularity in all the commands and it should work as well. However, the usage of Singularity is deprecated and the compatibility might be eventually broken.

Pre-installed components

Each image contains the fully-featured environment capable of running all the steps of the CaverDock workflow without any additional installations. Here we provide an overview of all installed software and commands.

List of pre-installed software:

  • CAVER

  • CaverDock

  • Discretizer

  • Gnuplot

  • MGLTools

  • pyCaverDock

List of available commands:

  • caver - wrapper for simple execution of CAVER)

  • caverdock - execution of the program for simulation of un/binding

  • cd-analyseeprofile - script for analysis of important energies in parsed energy profiles

  • cd-analysis - execution of the basic pipeline in a single command

  • cd-energyprofile - script for parsing data about discs and energies from the trajectory files

  • cd-extendtunnel - script for extension of discretized tunnels

  • cd-prepareconf - script for generating configuration file for CaverDock calculation

  • cd-reverseeprofile - script for reversing parsed energy profiles from inward binding calculations

  • cd-screening - execution of the virtual screening in a single command

  • discretizer - execution of the tool for tunnel discretization

  • prepare_ligand4 - script from MGLTools for conversion of ligand files

  • prepare_receptor4 - script from MGLTools for conversion of receptor files

First steps with Apptainer

The basic use of the image is pretty simple and does not require any advanced knowledge. The only thing to understand is the directory binding from your local computer to the running container (more technical details are available in the official documentation). By default, Apptainer mounts your current directory to the same path in the container, so it should not cause any troubles.

Generally, you can run your analysis in two basic ways:

  1. Run each command separately using apptainer exec:

    $ apptainer exec /path/to/caverdock.sif cd-extendtunnel -f tunnel.dsd -d 5 > tunnel-extended.dsd
$ apptainer exec /path/to/caverdock.sif mpirun -np 8 caverdock --config vina.config --out test.pdbqt --log caverdock.log --dump_bottlenecks bottleneck.dat
$ apptainer exec /path/to/caverdock.sif python3 custom_api_script.py

  2. Start an interactive shell inside the container and run commands there

    $ apptainer shell /path/to/caverdock.sif
Apptainer> cd-extendtunnel -f tunnel.dsd -d 5 > tunnel-extended.dsd
Apptainer> mpirun -np 8 caverdock --config vina.config --out test.pdbqt --log caverdock.log --dump_bottlenecks bottleneck.dat
Apptainer> python3 custom_api_script.py

Note

Apptainer is a very complex and flexible tool. To learn more, feel free to read the official Quick start guide.