By definition, the binding energy is the energy you need to disassemble the system in atoms. Therefore, if A, B and C are the atoms of the system, then BE=E(A+B+C)-E(A)-E(B)-E(C), where E(A), E(B) and E(C) is the corresponding energy for an isolated atom, and E(A+B+C) is the energy of the system. If A, B and C are not atoms, but parts of the system, the above equation is not correct.

Thank you Dr.Zacharias. The system has atoms as well as molecules ,so in this case how to calculate the binding energy??? Kindly provide me the formula if possible.

The simplest thing you can do is to follow the definition given above. Find the energy of the atoms of the system when they are isolated and subtract it from the energy of the system. However, if you think that it is more convenient for you and more helpful to present your resuts, you can give a different definition for the binding energy, subtracting from the energy of the system the energy of isolated molecules which constitute the system. In that case the binding energy values will not be the same, and you have to explain why it is more convenient to use this definition. In that case, your "binding energy" will be the energy to disassemble the system into molecules and not into atoms.