Hi,
there is a manual for calculate in the calculate directory (calculate_manual.pdf) which also describes how to add charges. Or check the list.example file which is an example input for calculate:
...
water.xyz
#
# same definition of water. The charge 0 is default.
#
h3o.xyz +1
#
# defines the h3o molecules with molecular charge +1
#
oh-.xyz -1
#
# defines the oh- anion with molecular charge -1
...