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 > -- > modeller-care@salilab.org https://salilab.org/modeller/ > Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage >