[modeller_usage] Re: Modeller is transforming ZN2 atom names to ZN

[Modeller Caretaker <>]

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
-- 
             https://salilab.org/modeller/
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