It's best to orient the protein before combining with the water box. Assume the protein is SEGID A, then
coor orient sele segid A end
will both center and rotate the protein, to align the longest dimension of the protein along the Cartesian X axis. To suppress the rotation, use
coor orient sele segid A end norot
See corman.doc for details on COOR ORIENT and other commands that manipulate or analyze coordinates.