If you’ve made the mistake of stripping all the water from a protein that had some crystal waters prior to solvation, you can generated a stripped topology file using parmed.
To do this follow:
$ $AMBERHOME/bin/parmed
> parm WT_protein_system_wat.prmtop
> strip :WAT,K+
> outparm strip.WT_protein_system_wat.prmtop
> quit
The bright side to having to use parmed is that you get to see some really adorable ASCII art.
There’s plenty more that parmed can do, so check out the documentation (and, if you use Python, the Python package).