How about
READ SEQU PDB SEGI WZ1 NAME waterbox.pdb
GENE WZ1 NOANGLE NODIHE
READ SEQU PDB SEGI WZ2 NAME WATERBOX.PDB
GENE WZ2 NOANGLE NODIHE

See also the testcase ~charmm/test/c39test/readpdb.inp

If all you have is water this should also work:
read sequ tip3 542
GENE WZ1 NOANGLE NODIHE
read sequ tip3 313
GENE WZ2 NOANGLE NODIHE


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden