[modeller_usage] modeling a complex

Dear friends, I have a pdb file containing coordinates for a complex of two subunits: subunits 1 in chain A and subunits 2 in chain B chain C and D contains fragments of another molecule that I don't care.

I want to model in the same time a molecule 1 on chain A and a molecule 2 on chain B so to build a model of the complex molecule1-molucule2 on the complex of the two subunits in the pdb file.

In which way I have to write down align file?

Tanks a lot Edoardo