Re: [modeller_usage] mutate_model on protein with ligand

[Modeller Caretaker <modeller-care@ucsf.edu>]

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
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