What is total charge in an atom?

The total or net charge of an atom is equal to: (the number of protons) - (the number of electrons).

The charge of a proton and electron are equal but opposite -- the proton is positive and the electron is negative. If protons and electrons are found in an atom in equal numbers, the net or total charge of the atom is 0 and thus, the atom is neutral. If there are more protons than electrons (positive charged) or if there are more electrons than protons(negative charged), then the atom is charged (and called an ion).

For example, an ion with 20 protons and 18 electrons has a charge of 20 - 18 = +2. This is the Ca⁺² ion.

a positive quark has a charge of 2/3, a negative quark has a charge of -1/3.
a proton has +1 positive, with 2 positive and 1 negative quark.