How to find molecular charge of fragments using quantum calculations?
Your question boils down to "where are the electrons" in a quantum chemical system?

The problem, is if there's any level of interaction between the two fragments, you don't know. The charge will be delocalized across the entire A+B complex.

Put it another way.. Let's say you have a bunch of atoms and you run a calculation and the overall charge on the molecule is +1. Where's the extra positive charge?

Well, you might make some guesses, but it's probably delocalized across multiple atoms. The same thing happens with intermolecular interactions, but to a lesser degree.

There are two approaches:


Constrained DFT: This is a method where you force the charge on a particular fragment to be the way you want. You can then compare this semi-localized charge with the distributed (unconstrained) calculation and compare.
Fragment MO: You can diagonalize the wavefunction onto multiple fragments that you define.


I don't use GAMESS much, but a quick search implies that FMO is supported in GAMESS.