# File/directory prepare for running haddock
**URL:** https://ask.bioexcel.eu/t/file-directory-prepare-for-running-haddock/1736
**Category:** HADDOCK
**Created:** [October 24, 2019, 3:06am UTC](https://ask.bioexcel.eu/t/file-directory-prepare-for-running-haddock/1736 "2019-10-24T03:06:58Z")
**Posts on this page:** 4
**Page:** 1
### Author:  [@zsip029](https://ask.bioexcel.eu/u/zsip029)
#### Post date: [October 24, 2019, 3:06am UTC](https://ask.bioexcel.eu/t/file-directory-prepare-for-running-haddock/1736/1 "2019-10-24T03:06:58Z")
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!
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### Author:  [@honoratorv](https://ask.bioexcel.eu/u/honoratorv)
#### Post date: [October 24, 2019, 7:21am UTC](https://ask.bioexcel.eu/t/file-directory-prepare-for-running-haddock/1736/2 "2019-10-24T07:21:03Z")
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/](http://www.bonvinlab.org/education/HADDOCK24/HADDOCK24-local-tutorial/)
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### Author:  [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)
#### Post date: [October 24, 2019, 7:33am UTC](https://ask.bioexcel.eu/t/file-directory-prepare-for-running-haddock/1736/3 "2019-10-24T07:33:29Z")
This one is for the new (not yet officially released version…).
Check also the instructions on [http://www.bonvinlab.org/software/haddock2.2/manual/](http://www.bonvinlab.org/software/haddock2.2/manual/)
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### Author:  [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)
#### Post date: [October 24, 2019, 7:36am UTC](https://ask.bioexcel.eu/t/file-directory-prepare-for-running-haddock/1736/4 "2019-10-24T07:36:35Z")
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)