If you want to find it theoretically, take the xyz coordinates from the crystal structure of these protiens, find single point energy for that conformation (using suitable basis set) for both the proteins (Let energy of protein1 be X and that of other protein2 be Y). DO the same for the structure in which these two proteins are interacting (Let this energy be Z). Then to calculate the binding energy, just do the following mathematics:

Binding energy = Z - (X+Y)

These calculations will be faster if u already have the xyz's of all the structures from X-ray diffraction as optimizing these molecules from scratch will be computationally very expensive.

You can have a look at the following link.

http://ambermd.org/#AmberTools

The above tools are used with a MD trajectory of the complexes.

For simple estimations (free energy of dissociation) you may try PISA:

http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html

Which tool you have used for docking? whatever tool you r using there they have definitely give the binding energy. if that is not the case then what you do, use the dock structure and perform molecular dynamics simulation.Then Calculate the binding free energy of a protein-ligand complex using MM-GBSA

– From energy minimized structures or

– From a molecular dynamics trajectory

After that use PB(GB)SA free energy method that will decompose binding energy into all these components including interaction terms by following equation

∆Gbind= Gcomplex- Gligand- Gprotein

G = + + + -T∆S

Thank you all for valuable suggestions.