There are two types of charge on an atom 1st is a partial charge(due to electronegativity), and 2nd is formal charge.
partial charge & formal charge define together or
Is there any other way to define formal charge on atom separately?
eg. Hydronium ion H3O+ in this +1 positive charge is formal charge
Classical non-polarizable force fields use an “effective charge” that is a combination of all charge effects. How to determine this effective charge is part of the force field parameterization “recipe”.
For ionic molecules, the sum of the partial charges typically adds up to the formal charge of the molecule. For individual atoms the (formal) charge of the atom core and the associated electrons is irrelevant, since those are integrated out. After all, these are classical models.