As you can see from the error message your system contains too many possible hydrogen bond acceptors, and you may also end up with too many atoms; for a system this big you need to install CHARMM with at least the large option. The version you are currently using was installed with the medium option. Since you seem to be using CHARMm (rather than CHARMM) I am not sure how you select a large version of the program. If you cannot do this you may have to make do with only 8A between the solute and the boundary, which still leaves 16A between the solute and its image.
The issue about adding ions has been discussed a few months ago on this forum.