# Command not found HADDOCK binding site screening tutorial **URL:** \ **Category:** HADDOCK\ **Created:** [April 29, 2020, 3:14pm UTC](https://ask.bioexcel.eu/t/command-not-found-haddock-binding-site-screening-tutorial/1976 "2020-04-29T15:14:13Z")\ **Posts on this page:** 9\ **Page:** 1
**Author:** ![Leo](https://avatars.discourse-cdn.com/v4/letter/l/c2a13f/32.png) [@Leo](https://ask.bioexcel.eu/u/Leo)\ **Post date:** [April 29, 2020, 3:14pm UTC](https://ask.bioexcel.eu/t/command-not-found-haddock-binding-site-screening-tutorial/1976/1 "2020-04-29T15:14:13Z")
I currently am trying to follow the tutorial " HADDOCK small molecule binding site screening" with my own protein-ligand docking run. I get to the step where am I going to run the following command using tcsh shell: $WDIR/encode-contacts.csh structures/it0/Acontacts.lis AcrB\_contacts.pdb However, when I run it I instead get the following message: /home/leo/HADDOCK-binding-sites-tutorial/ana\_scripts/zone\_b: Command not found I´ve been inside the ana\_script directory and run the commands “make” and “source setup.csh” which both were successful and I´ve also performed chmod + x Zone\_b. Still, I get the same error message. This has been posted before in this forum ([Error when running $WDIR/encode-contacts.csh structures/it0/Acontacts.lis AcrB\_contacts.pdb](https://ask.bioexcel.eu/t/error-when-running-wdir-encode-contacts-csh-structures-it0-acontacts-lis-acrb-contacts-pdb/640/5)) but noone of the suggested solutions in that thread worked for me Could anyone possible help me out? ---
**Author:** ![honoratorv](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/honoratorv/32/672_2.png) [@honoratorv](https://ask.bioexcel.eu/u/honoratorv)\ **Post date:** [April 29, 2020, 3:48pm UTC](https://ask.bioexcel.eu/t/command-not-found-haddock-binding-site-screening-tutorial/1976/2 "2020-04-29T15:48:42Z")
Sorry for the naive question but does this path exist in your system? `/home/leo/HADDOCK-binding-sites-tutorial/ana_scripts/zone_b` ---
**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\ **Post date:** [April 29, 2020, 3:57pm UTC](https://ask.bioexcel.eu/t/command-not-found-haddock-binding-site-screening-tutorial/1976/3 "2020-04-29T15:57:16Z")
There are two executables provided for zone\_b, one for Linux, one for MacOSX. On which system are you running? You might also try to install our PDB-tools (see [https://github.com/haddocking/pdb-tools](https://github.com/haddocking/pdb-tools) ) and use those (modifying the scripts or writing your own). We also have now a beta version of a PDB-tools web server available at: [https://bianca.science.uu.nl/pdbtools/](https://bianca.science.uu.nl/pdbtools/) ---
**Author:** ![Leo](https://avatars.discourse-cdn.com/v4/letter/l/c2a13f/32.png) [@Leo](https://ask.bioexcel.eu/u/Leo)\ **Post date:** [April 29, 2020, 5:07pm UTC](https://ask.bioexcel.eu/t/command-not-found-haddock-binding-site-screening-tutorial/1976/4 "2020-04-29T17:07:06Z")
I am really inexperienced with code so I dont know how to modifiy or create scripts. I am using a linux operative system atm. It would be really nice if this worked since I think it is a really cool application. ---
**Author:** ![Leo](https://avatars.discourse-cdn.com/v4/letter/l/c2a13f/32.png) [@Leo](https://ask.bioexcel.eu/u/Leo)\ **Post date:** [April 29, 2020, 5:08pm UTC](https://ask.bioexcel.eu/t/command-not-found-haddock-binding-site-screening-tutorial/1976/5 "2020-04-29T17:08:33Z")
No, not that particular PATH. But the WDIR is coupled to ana\_scripts since I sourced the setup.csh ---
**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\ **Post date:** [April 29, 2020, 5:35pm UTC](https://ask.bioexcel.eu/t/command-not-found-haddock-binding-site-screening-tutorial/1976/6 "2020-04-29T17:35:05Z")
Test if the linux executable is working. If it is create the proper link Probably time to invest in learning more of linux and scripting - there is no free lunch 🙂 A good starting point is for example the tutorials from [softwarecarpentry.org](http://softwarecarpentry.org) ---
**Author:** ![Leo](https://avatars.discourse-cdn.com/v4/letter/l/c2a13f/32.png) [@Leo](https://ask.bioexcel.eu/u/Leo)\ **Post date:** [April 29, 2020, 7:13pm UTC](https://ask.bioexcel.eu/t/command-not-found-haddock-binding-site-screening-tutorial/1976/7 "2020-04-29T19:13:05Z")
I am currently doing my bachelor thesis and have limited amount of time. I do want to learn the coding aspect more later but now I am in a need of help. Didn´t I already create the proper link when I sourced setup.csh? How do I test if the linux executible is working? ---
**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\ **Post date:** [April 30, 2020, 8:53am UTC](https://ask.bioexcel.eu/t/command-not-found-haddock-binding-site-screening-tutorial/1976/8 "2020-04-30T08:53:26Z")
Well - probably the best in this case is to find someone around you with some Linux expertise. ---
**Author:** ![Leo](https://avatars.discourse-cdn.com/v4/letter/l/c2a13f/32.png) [@Leo](https://ask.bioexcel.eu/u/Leo)\ **Post date:** [April 30, 2020, 6:24pm UTC](https://ask.bioexcel.eu/t/command-not-found-haddock-binding-site-screening-tutorial/1976/9 "2020-04-30T18:24:40Z")
Okey, thank you for your answer.