On 2/27/23 10:22 AM, Pedro Guillem via modeller_usage wrote: > I'm using modeller to mutate a single residue in a PDB template that > contains ZN atoms. > > The mutation is taking place correctly, but the resulting PDB is written > with the name ZN instead of ZN2, which is in the original template. My > ZN is in a different coordination state and I need the name to stay > ZN2 in the mutated structure.
Yes, Modeller treats the ZN2 residue type as a synonym for ZN. This is defined in the modlib/restyp.lib file in your Modeller distribution. If you like, you can modify this file to remove the synonym, i.e. find the line
HETATM | ZN ZN2 | z | | ZN2 | zinc, +2
and replace with
HETATM | ZN | z | | ZN2 | zinc, +2
Modeller will then treat ZN and ZN2 as two different residue types. Since it then won't recognize ZN2, it will treat it as a rigid body, which is probably fine for your application, although you could add a new ZN2-specific residue type if you want as per https://salilab.org/modeller/FAQ.html#8
Ben Webb, Modeller Caretaker