This script analyzes the total partial charge and total formal charge for each residue. Residues for which the formal and partial charge do not match are reported.
Also, selections of part of a residue return the total charge for that selection. This is very helpful when making manual changes to atom charges in order to make the residue charge an integer.
The script also returns the total formal and partial charge for the molecule amd creates residue and molecule properties with the total charges.
Note, to fix residue formal and partial charge mismatches try "fix_charges" here

http://community.accelrys.com/message/1638

Integer total charge, and in some cases zero total charge, is recommended in all energy simulations.
This script provides essential information to determine what to change to address the CHARMm warning that the total charge (of a residue or group) is not an integer.

*However, there are some cases where formal charge and partial charge may not be the same and some cases where a residue's partial charge is not intended to be an integer. For example, this is done intentionally for the 5' and 3' termini of DNA residues. With that said the total partial charge for any molecule should be an integer value, and if it is not charges should be adjusted.