| -select CA | Atom selection (default all). |
| -rename D | Rename molecules from the given letter. |
| -verbose 7 | Verbosity of output. |
| -box 10,10,10 | Size of enclosing box (angstrom, default from coordinates). |
| -pbc | Resolve periodic boundary bonds before catenation. |
| -parameters parm.star | Atomic properties parameter file (default atom_prop.star). |
| -output output.pdb | Output coordinate file (default temp.pdb). |