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).