[modeller_usage] leave out termini of a structure

Dear users,

I have four similar structures. They are aaa.pdb, bbb.pdb, ccc.pdb and ddd.pdb. Unfotunately, the first 15 residues of of all the structures are missing. I modelled the aaa.pdb using aaa.pdb, bbb.pdb, ccc.pdb and ddd.pdb. When I modelled aaa.pdb, a loop of aaa.pdb goes through the rest of the protein. i.e. occurs knot. My friend said "you should leave out the termini". How will I leave out termini of a structure with Modeller? What do you suggest?

Thanks in advance