
Just run the following command:

   packs protein.pdb water.gro -ci Cl.gro -nm 2500 -it -bk

to use the local files, or

   packs protein.gro spce_oplsaa.wtr -ci Cl_oplsaa.ion -nm 2500 -it -bk

to use the geometry and force field files from the database.

This will create:

   protein+water-Cl_mol2500.gro
   protein+water-Cl_mol2500.top
   protein+water-Cl_mol2500.zip

To visualize the simulation box, try:

   sview protein+water-Cl_mol2500.gro
   jmol protein+water-Cl_mol2500.gro
   vmd protein+water-Cl_mol2500.gro

Note that in this example, protein force field files are created throughout the packaging process.
