The basic mode of using Facio for PDB file processing is this.
1. Provide a PDB file (possibly, not protonated).
2. Open it with Facio, and save as HETATM/CONECT PDB file.
This is necessary to rewrite your PDB in the way Facio likes (menu: File).
3. Reopen it with Facio, and complete the structure by adding H if
necessary (Menu: Utilities).
4. Save as HETATM/CONECT and reopen.
5. Now you can fragment: go to menu: FMO(GAMESS) and click a few buttons.
You can add manual fragmentation too.
6. Add GAMESS options ("Show FMO input options"), and voila - you have a file
you can submit for calculations.
7. Next time, you can just read this PDB and go directly to (5).