Before using HADDOCK3, install HADDOCK3 following the installation instructions.


This is a minimal description of how to run HADDOCK3. We are currently creating detailed documentation and tutorials. The minimal HADDOCK3 execution command is:


Where the <CONFIG WORKFLOW> is a haddock3 configuration file describing the simulation workflow.

You can inspect all haddock3 options with:

haddock3 -h

Inside the HADDOCK3 main folder, there is an examples/ folder. There you will find several subfolder with examples for specific docking scenarios. Please experiment running those configuration files ending in -test.cfg. For example:

cd examples/docking-protein-protein
haddock3 docking-protein-protein-test.cfg

Feel free to open the cfg files with your preferred test editor, these are plain text files.

To get the list of all possible parameters for each module:

haddock3-cfg -h
haddock3-cfg -m <MODULE NAME>
haddock3-cfg -m rigidbody

We are actively working towards expanding our documentation pages. Thanks for using HADDOCK3! For any question please open an issue here.