File/directory prepare for running haddock

HADDOCK
1

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 RemoveBadPDB.py, Keeplive.py 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!

2

Hi! Maybe you missed some steps of the installation, please check this link (its similar for 2.2): http://www.bonvinlab.org/education/HADDOCK24/HADDOCK24-local-tutorial/

3

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

Check also the instructions on http://www.bonvinlab.org/software/haddock2.2/manual/

4

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)