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 -- modeller-care@salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage