Re: [modeller_usage] mutate_model on protein with ligand

On 11/18/13 3:21 AM, Anna Marabotti wrote: > I used mutate_model.py to introduce a single point mutation into the > structure of my protein with a ligand bound into the active site. The > mutation I introduced was near the ligand, and when I had a look at the > resulting structure, I saw that the mutated residue has been located in > too strict proximity with the ligand

This is because Modeller has no parameters for the protein-ligand interaction. You would need to add suitable distance restraints.

> can I simply replace HETATM with ATOM in > order to make mutate_model.py correctly functioning?

No. It still wouldn't know what that residue is.

Ben Webb, Modeller Caretaker