Electrostatic interactions are probably overestimated.

Modeling metal ions is tricky and system-specific. One model will not work for all systems. This is just one of the anecdotal evidence for why no molecular modeling tool can be reliably used in a black-box fashion.

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If the metal ion is treated quantum-mechanically (QM), it will still interact with the molecular-mechanically (MM) modeled part in the QM/MM model. Are there any charged amino acid residues in the inner MM part? Can you decompose the metal-protein interaction energy into contributions from individual amino acid residues?

By defining the entire system with an MM model, one can play with the model of the metal (charge, size, structure); see the attached link for some examples . . .

http://ambermd.org/tutorials/advanced/tutorial20/

Dear Dr. Martin Klvana

you are absolutely right in pointing out that in heavy metals interactions electrostatic component is overestimated..That what, I figured out by analyzing the interaction components.

But, I was unable to figure out how come the electrostatic component of heavy metal is disturbing the Interaction energy of the System (Protein-ligand), as I have treated the heavy metal to be without charge and in case of heavy metal complex, i have covalently linked it to complex.

There are no charged amino acid residues in the inner MM part.

I am not sure how to decompose the metal-protein interaction energy into contributions from individual amino acids, but I will go through the tutorial and try to implement it, on my studies.

Thanks and regards

Tanuj Sharma..