Unfortunately Haddock does not have the proper tutorial as its site indicates that tutorial site is under construction and if you have prepared the AIR files and then you have to prepare the "run.cns" (Example script is given in the site) after preparing this run.cns file you can start the calculations.

If you are unable to perform the docking in standalone way its better to use the Haddock webserver. Currently most of the users are using the Haddock web server which is very popular in research community and its e-NMR integrated site is accessible to the users with GRID certificate.

This e-NMR integrated Haddock webserver is very fast and gives results as fast as the stand alone version installed normal workstations (High end workstations might be able to produce the results faster than this as well) and this webserver has all the options which can be used while performing the docking calculations

http://haddock.science.uu.nl/enmr/services/HADDOCK/haddock.php

@Aravind : I think you have installed the Haddock stand alone version in your Linux machine and trying to perform the protein-protein docking. or else you are trying the Haddock webserver..? please elaborate your query..!!

I installed the haddock properly, even i changed the envir_variable. But unable to get the step by step tutorial and commands.

Unfortunately Haddock does not have the proper tutorial as its site indicates that tutorial site is under construction and if you have prepared the AIR files and then you have to prepare the "run.cns" (Example script is given in the site) after preparing this run.cns file you can start the calculations.

If you are unable to perform the docking in standalone way its better to use the Haddock webserver. Currently most of the users are using the Haddock web server which is very popular in research community and its e-NMR integrated site is accessible to the users with GRID certificate.

This e-NMR integrated Haddock webserver is very fast and gives results as fast as the stand alone version installed normal workstations (High end workstations might be able to produce the results faster than this as well) and this webserver has all the options which can be used while performing the docking calculations

http://haddock.science.uu.nl/enmr/services/HADDOCK/haddock.php

Can you explain what you did exactly?

Did you create new.html file?

and then 

run.cns?