It can be shown that the total energy of the universe would also be zero if it is created by some supernatural agent. Let us say that this supernatural agent is God. Now what does it mean that the universe has been created by God? As universe primarily means its space, time, matter and energy, so universe created by God will mean its space, time, matter and energy have been created by God. That will further mean that before creation by God there was no space, no time, no matter and no energy. That will again mean that God was in no space and time and that God did not contain any matter and energy. That is the reason as to why theists always describe their God as spaceless, timeless and immaterial. (There are some atheists who failing to grasp this simple logic raise question about this spaceless, timeless and immaterial God. But a creator God can never be anything other than spaceless, timeless and immaterial, because this is the one and only one logically possible consequence of being the creator of a universe.) Neither this spaceless, timeless and immaterial God can contain any energy, because energy was also created by God only along with the creation of the universe. That means the total energy content of God is zero. Therefore the total energy content of the universe will also be zero, because universe cannot contain more energy than the source from which it has originated.
Here it might be objected that neither energy nor matter can be created or destroyed. But if we keep in mind that the total energy of the universe has always remained fixed at its zero value, then we can say that as such energy has not been created or destroyed at all. Only that it has taken positive and negative forms in the universe, the total energy always remaining zero. The same can be said about matter also.
This once again shows that the reasoning of Lawrence Krauss is faulty when he has argued that as because the total energy of the universe has been found to be zero, so from this it can be concluded that the universe has originated from nothing.1 But here we have shown that the total energy of the universe will also be zero even if it is created by God. So once again it is established that zero total energy cannot be the only criterion on the basis of which it can be concluded that the universe has originated from nothing.
Reference:
1. http://scigod.com/index.php/sgj/article/view/449/498