Dear Zarrin, Thanks for your interest in my question and for your valuable information.

You can also rename the other protein to chain B in MOE (or save it as a PDB and rename it using a text editor). MOE can then calculate a non-bonded interaction energy score, which sums up the strength of the VDW and electrostatic interactions using whatever force field you've selected. Doesn't calculate actual free energy differences, but the non-bonded interaction energies are good enough to compare the strength of the interacton.

Hi,

Try PDBsum (http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=index.html). Upload your pdb model with chain A and B clearly differentiated. Use the generate option at your left to upload the pdb file of your complex. You will receive a code in your email. Use the protein-protein option to see all the contacts.

Alternatively, in Moe use the Measure/Protein Contacts option in the SEQ window.

Good luck!

THANKS FOR ALL OF YOU DUE TO YOUR FRUITFUL ANSWERS.

Dear A.S.A,

PDBSum would be the better option, since it is authenticated and freely available

Dear colleague,

By using the MOE sequence editor, select each chain and save as separate (.mol2) files. The close the MOE window and reopen. Open both files in the same window (they superpose on the screen), then save as a single file now. MOE will now be able to differentiate between the two.

Thanks

Fidele

Thank you Fidele .. I am grateful.

you can use ligplot+

http://www.ebi.ac.uk/thornton-srv/software/LigPlus/

try Acceryls Discovery Studio!! you could easily find the option of monitor the intramolecular interaction 

Under the Proteins menu there is an option called 'Contacts'. This will list the interactions between proteins. You can choose to list the interactions between the same protein chains or, for your case, choose to list interactions between different chains.

Hope this helps!