I suggest you to use gromacs.

for sung that install gromacs and run the following commands to get the structure with water:

gmx pdb2gmx -f protein.pdb -o processed.gro -water tip3p

after that enter this :

gmx editconf -f processed.gro -o boxed.gro -c -d 1.0 -bt triclinic

gmx solvate -cp boxed.gro -cs spc216.gro -o solvated.gro -p topol.top

the "solvated.gro" is your file with water in a box 1.0 angestrom distance of each side and solved with water. open this file in pymol or chimera and save in pdb format or each format you want.