Dear Clarke,

To calculate the interaction energy, u have to perform MD simulation of your system and then perform MMGBSA or MMPBSA using MD generated trajectory.

MD simulation using Gromacs: http://www.gromacs.org/Documentation/Terminology/Molecular_Dynamics_Simulations

Gromacs tutorial:

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/

MMPBSA:

http://rashmikumari.github.io/g_mmpbsa/Tutorial.html

Regards 

Nandan

hi Clarke

As suggested by Nandan, Binding free energies can be calculated (molecular mechanic (MM), electrostatic contribution to solvation (PB) and nonpolar contribution to solvation (SA)), using MM/PBSA tool. But, for our protein protein system, the tool was unable to perform calculation, so we carried out calculation using QM/MM tool of Discovery Studio and GMX-PBSA tool, both of them comparitive results.

But first, you need to perform MD studies on protein-protein complex, in presence of Metal Cation and in absence of Metal Cation. On the basis of Binding energy analysis you can rank the relative affinity of two proteins, in presence and absence of metal ion.

If you are interested in studying how the Metal ion interact with individual amino acids, then you may have to perform DFT studies on the system (consisting of amino acids interacting with Metal ions). This will give you a deep insight of what kind of electronic perturbation are created by metal ions on the interacting amino acids.

regards

Tanuj Sharma

Thank you Nandan and Tanuj for your help

It's my pleasure