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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
--
             http://www.salilab.org/modeller/
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