[modeller_usage] Using 2 templates, one to just model the protein and the other to just model the ligand

Dear MODELLER users,

I want to do homology modelling of a protein based on just one template because it is so far the only template of a particular protein state of its family I' m interest in. However, that template does not contain the natural ligand of the target. Then, I want to use another template of the protein-ligand(natural) complex of interest but just to say Modeller to use the ligand coordinates. So, it is a multi-alignment using the HET option but I don't know how to say Modeller that I just want to model the target sequence based on just one template and considering the ligand of the other template. Is this possible?

I look forward to hearing from you.

Juan C. Munoz-Garcia, PhD