Hi Yann, can you post  a screenshot of the error message? It should be
stated there which are causing problems.

Very often the problems are hydrogens. So just delete those. One easy
way is to do is to open in coot and when saving there is a tick box
without hydrogens. There are also tools in phenix doing this.

Also you can submit the pdb to PDB_REDO to check if there are more sever
problems. If PDB_REDO runs then there are no big errors. Then just use
the output for phenix refine.

And as Xavier wrote ligands also can cause problems. But also there most
times the hydrogens.

Br, Georg.


Am 2025-01-30 um 4:26 PM schrieb yannlefrancoiscopy@gmail.com:
> Hello,
> I'm a newbie phenix user, and i was trying to refine a model.
>
> and when i tried to refine it, I got an error message saying that some atoms had unknown nonbonded interaction.
>
> However, there are no indication to which one are problematic, Any tips on how to find the problematic one and how to correct them  ?
>
> best wishes,
> Yann
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