Haddock server is the best one i will suggest this ..............it is freely available. Where you can find protein-DNA, protein-protein interaction. Link is provided............

http://haddock.science.uu.nl/

You can use Autodock - Vina. Its freely available, downloadable and easy to use. You will also need MGL Tools 1.5.6 and Pymol or Ligplot to draw the docked structures and see the interaction between amino acids and the ligand.

vina.scripps.edu/download.html

http://mgltools.scripps.edu/downloads

www.pymol.org

you can use dock6 that is especially design for protein ligand docking. its freely available for academics. for visualizing software you can use chimera. it's much easier  than Pymol.

u can download it from below mention link

http://dock.compbio.ucsf.edu/

dock6 tutorial.

http://ringo.ams.sunysb.edu/index.php/2012_DOCK_tutorial_with_Streptavidin

If you would like to do Protein-Protein docking then you could use Hex, which is fast and has lot option..

http://hex.loria.fr/dist/index.php  

Autodock and Autodock Vina.

you can use swissdock server. It is  a free protein ligand docking web service powered by EADock DSS by the Molecular Modeling group of the Swiss Institute of Bioinformatics. plz follow the link for online docking.....

www.swissdock.ch/

sample research paper (reference) on result of swissdock server

Hetal, K. P.; Ratna, A. T.; Pratibha, B. D. Docking Studies of Components of Tulsi and Mamejavo against Plasmodium Lactate Dehydrogenase. International Research Journal of Biological Sciences 2013, 2, 8–12.

Kumar, V.; Kumar, C. S.; Hari, G.; Venugopal, N. K.; Vijendra, P. D.; B, G. B. Homology modeling and docking studies on oxidosqualene cyclases associated with primary and secondary metabolism of Centella asiatica. SpringerPlus 2013, 2, 189.

AutoDock.

KIndly Use AutoDock

Download HEX 8.0.0.  Most suitable for the people who are not working in the core field of Drug designing but needs to do some docking for other purpose...

Very easy but good prediction...you will find many simple case of virtual screening is done in this tools..

http://hex.loria.fr/hex.php

Dear kamalesh,

what is the meaning of value -1.00 in hex output as mention below.

# Docking file generated by Hex 6.9 + CUDA

# ReceptorSourceFile: /home/orpailleur/ritchied/hex_tmp/hex_jobs/54f6848a1f2ca/files/r54f6848a1f2ca.pdb

# LigandSourceFile: /home/orpailleur/ritchied/hex_tmp/hex_jobs/54f6848a1f2ca/files/l54f6848a1f2ca.pdb

# ComplexSourceFile: None

#

# Apply Euler rotation (alpha,beta,gamma) to ligand, then translate by (x y z)

#

# Format: Cluster Solution RMS Etotal x y z alpha beta gamma receptor-model ligand-model

#

# -----------------------------------------------------------

#

1 1 -1.00 -895.45 -0.038046 -0.099732 0.422465 1.570796 0.000000 1.570796 1 1

2 4 -1.00 -766.62 112.484146 55.693127 24.802420 2.723282 1.236829 2.010645 1 1

3 9 -1.00 -707.28 49.450123 44.766552 12.209818 3.576699 0.541959 1.819376 1 1

Dears, any one can add a link of AutoDock tutorial/guide for its usage?

Thanks Abdul kadir

Sorry for answering late....

This might be helpful for you...

The "-1" means nothing was calculated. You will always see this value unless you enable

Backbone Bumps in the Postprocessing selector in the Docking Control panel. In that case,

each orientation will be checked for steric clashes between backbone atoms (the column

will show the total count of bumps). You can then use the Clustering control panel to

put solutions with more than a given number of bumps to the end of the list, if you wish.

Requesting molecular mechanics (MM) energies also causes backbone bumps checking to

be turned on. Similarly, "Hbonds = -1" means no hydrogen bonds were calculated. You

need to enable the Show H-bonds toggle in the Molecule Control panel.