I want to do homology modelling (using MODELLER) 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 with MODELLER?
I think that what you want to do is to use both structures as a template. Modeller lets you use only part of a structure as a template so set the file up to use all of the first structure and then just the ligand of the second structure, its probably a separate chain so easy to figure out.
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