Awesome Ben, thank you so much for your reply!!!
As long as the atom name is the same it will be fine.

I just modified restyp.lib like you suggested but the output PDB is still generated with ZN only.
I also deactivated/activated the conda environment (where modeller is installed). I tried both env.io.heatatm True and False.

ORIGINAL:
ATOM    599  ZN  ZN2 A  74      28.353 -59.777  92.760  1.00  0.00          ZN  
ATOM    600  ZN  ZN0 A  75      40.834 -53.893  90.903  1.00  0.00          ZN  
ATOM    601  ZN  ZN2 A  76      26.392 -65.030  97.280  1.00  0.00          ZN  

POST-MODELLER:
HETATM  600 ZN    ZN  A  74      28.353 -59.777  92.760  1.00  0.00          ZN
ATOM      601 ZN   ZN0 A  75      40.834 -53.893  90.903  1.00  0.00          ZN
TER         602 ZN0 A  75
HETATM  603 ZN    ZN  A  76      26.392 -65.030  97.280  1.00  0.00          ZN

Any hints?
Pedro

El lun, 27 feb 2023 a las 20:24, Modeller Caretaker (<modeller-care@salilab.org>) escribió:
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
--
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