This small problem had been solved.

Prof. Alexandre Bonvin helpful comment:

“ Make sure to specify the correct location of the cns executable in run.cns (you edit the installation run.cns in the protocols dir).

Look for cns_exe. It should point directly to the executable ”

Hadoock creates a directory runX (where X is the run number defined in the new.html file). In this directory, a run.cns file is then created.

http://www.nmr.chem.uu.nl/haddock/run.html

The run.cns file contains all the parameters to run the docking. You need to edit this file to define a number of project-specific parameters such as the number of structures to generate at the various stages etc. And also the path to cns executable (cns_exe)!!!

$ which cns

/usr/local/cns_solve_1.3/intel-x86_64bit-linux/bin/cns (in my case)

edit the run.cns file (runX folder):

{===>} queue_1="csh";

{===>} cns_exe_1="/usr/local/cns_solve_1.3/intel-x86_64bit-linux/bin/cns";

{===>} cpunumber_1=4;

Surprisingly (for me), under Ubuntu you must apparently change the path to cns_exe also in the installation run.cns file found in the protocols (…/haddock2.1/protocols/)

Thank you Arslan for your concern and Alexandre Bonvin for kindly provide a solution.

I will give you a bite more of information!

Before I started installing and runnig Haddock/CNS the following packages

were installed:

-pynton (version 2.7)

-tcsh/csh

-the intel fortran compiler (to compile cns, gfortran does not seem to work)

-flex

-perl

-gcc

-gawk

For CNS a binary installation is available for Intel i686, x8_64.

http://www.msg.ucsf.edu/local/programs/cns1.3/

This version was compiled using ifort obtained from

http://software.intel.com/en-us/non-commercial-software-development.

Once the CNS environment variables were set up, CNS was launched with

any error messages

For haddock

I requested a copy of version 2.1 from Prof. Alexandre M J J Bonvin.

http://www.nmr.chem.uu.nl/~abonvin/

To install hadoock I just uncompress the following file

tar xvfz haddock2.1.tgz

and source the haddock_configure.csh under tcsh shell

Haddock reads well the cgi scripts (new.html) and creates the run1 folder

with the file run.cns inside.

I had change the toppar files from 5.3 (default in run.cns) to 5.4 (must

be 5.4 if you use CNS 1.3). The path of CNS in run.cns was always modified

before running HADDOCK.

When typing haddock2.1 inside run1 the following outcome is obtained:

....

$looking for existing files

$ waterdock false

$ generating PSF and PDB file of protein A with the command:

$ queue command:

$ generating PSF and PDB file of protein B with the command:

$ tcsh /usr/local/haddock2.1/examples/barnase-barstar

$ /run1/barnase->barstar_run1_generate_A.job

$ queue command:

$ waiting for the psf files...

$ tcsh /usr/local/haddock2.1/examples/barnase-barstar/run1/barnase-

$ barstar_run1_generate_B.job

$ QUEUE_DOWN

$ protocols/cns1: Command not found.

$

$ Queue command failed, retrying in 15 seconds

$ QUEUE_DOWN

$ protocols/cns1: Command not found.

(then freezes)

or in a second attempt (typing again haddock2.1)

$ looking for existing files

$ ln: failed to create symbolic link `protocols/cns1': File exists

$ waterdock false

$ waiting for the psf files...

(then freezes)

Thanks in advance.

This small problem had been solved.

Prof. Alexandre Bonvin helpful comment:

“ Make sure to specify the correct location of the cns executable in run.cns (you edit the installation run.cns in the protocols dir).

Look for cns_exe. It should point directly to the executable ”

Hadoock creates a directory runX (where X is the run number defined in the new.html file). In this directory, a run.cns file is then created.

http://www.nmr.chem.uu.nl/haddock/run.html

The run.cns file contains all the parameters to run the docking. You need to edit this file to define a number of project-specific parameters such as the number of structures to generate at the various stages etc. And also the path to cns executable (cns_exe)!!!

$ which cns

/usr/local/cns_solve_1.3/intel-x86_64bit-linux/bin/cns (in my case)

edit the run.cns file (runX folder):

{===>} queue_1="csh";

{===>} cns_exe_1="/usr/local/cns_solve_1.3/intel-x86_64bit-linux/bin/cns";

{===>} cpunumber_1=4;

Surprisingly (for me), under Ubuntu you must apparently change the path to cns_exe also in the installation run.cns file found in the protocols (…/haddock2.1/protocols/)

Thank you Arslan for your concern and Alexandre Bonvin for kindly provide a solution.