File/directory prepare for running haddock

Hi, everyone!
I am new for protein docking and haddock. Now I am try to run haddock in my cluster. I had submit my job to web server and know something about it. But I am still confused and lost in manual after learning for a while.
The biggest question is that when I try to run haddock in my computer, I find I need to copy files to the coorresponding directory. for example: I need to copy files like, to protocols/ and check-error-message.csh to tools/. And in it0 stage calculation, it failed. Because it can’t find complex_1.pdb file in structure/it0/ which is in begin/. I think in the running, the pdb file generated in begin/ will be copied or moved to structure/it0 automaticly, rathan than maunally. I don’t konw what mistake I had made.
Another question is that before running, I must build begin, data, data/sequence, protocols, tools, toppar, structure, structure/it0, structure/it1 directory? they will not built by the script?

Thanks for your time. And appreciate for any reply!

Hi! Maybe you missed some steps of the installation, please check this link (its similar for 2.2):

This one is for the new (not yet officially released version…).

Check also the instructions on

But we also have a chapter describing the local use of HADDOCK:

• J.P.G.L.M Rodrigues, E. Karaca and A.M.J.J. Bonvin. Information-driven structural modelling of protein-protein interactions. Methods in Molecular Biology: Molecular Modelling of Proteins. Ed. Andreas Kokul. Humana Press Inc. 399-424 (2015).

Preprint attached

(Attachment ProteinProteinInteractions_preprint.pdf is missing)