Command not found HADDOCK binding site screening tutorial

HADDOCK
1

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) but noone of the suggested solutions in that thread worked for me

Could anyone possible help me out?

2

Sorry for the naive question but does this path exist in your system? /home/leo/HADDOCK-binding-sites-tutorial/ana_scripts/zone_b

3

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 ) 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/

4

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.

5

No, not that particular PATH. But the WDIR is coupled to ana_scripts since I sourced the setup.csh

6

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 :slight_smile:

A good starting point is for example the tutorials from softwarecarpentry.org

1 Like
7

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?

8

Well - probably the best in this case is to find someone around you with some Linux expertise.

9

Okey, thank you for your answer.