Dear Verma, for prediction of Van der Waals interactions, hydrogen bridges and other weak interactions, you can use Schrodinger library. Stefan.

A software to evaluate non bonded interactions is HINT (Kellogg et al. ) that consider both entropic and enthalpic contributions

You can use autodock or schrodinger as well

The NAMD Energy plugin to VMD will do this. You'll need VMD and NAMD installed. http://www.ks.uiuc.edu/Research/vmd/plugins/namdenergy/

there is the software GOLD, it can predict the hydrogen and the Van der Waals interactions

Merzoug mam , i think that gold is only for genome annotation and comparative study....can u clear this doubt?

GOLD is one of the most used molecular docking programs.it is used to predict and in reproduce the protein (ex, enzyme) ligand interactions. it can predict the hydrogen and the Van der Waals interactions

Disclaimer: I work for the CCDC

GOLD is a protein-ligand docking package maintained by the CCDC (Cambridge Crystallographic Data Centre). It can be used both for pose prediction and virtual screening.

http://www.ccdc.cam.ac.uk/products/gold_suite/

Below is a link to some of the scientific publications describing GOLD.

http://www.ccdc.cam.ac.uk/support/product_references/#gold

Good luck with your work.

Tjelvar

Thank you very much to all of you for relying .....