The Molecular Graphics Laboratory Forum

I tried calculating energy contributions from two proteins in a protein complex separately using epdb keyword. The energy results from each don't add up to the total energy from the complex computed from docking ligands to the complex previously even though the same ligands are being used. Example: One ligand docked to the complex has energy -17kcal. When separate energies are calculated for the two proteins in the complex with the same ligand, one is +0.14kcal and the other is -2kcal. They should add up to -17kcal but they don't. Is there some way around the problem. Does anyone know why the energies don't add up? Thanks in advance.

[ this discussion is a follow up of this thread ]

Hi,

the fact you have a positive energy means that there is some unfavorable interaction (i.e. overlap) of one or more ligand atoms with the target structure. while the other interaction seems to be very weak. I suggest you to double-check that the splitted structures obtained from the original one include all the atoms.
Also, it would be useful to visually inspect the structures to be sure the same atoms from each part are still in close contact with the ligand used in the EPDB calculation.

Stefano