On Jul 9, 2026, at 8:05 AM, Bruno Hay Mele via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi,

I am trying to minimize an AF3-generated protein–RNA complex [1, attached] in ChimeraX [2,3] , but the minimization fails with the following error:

`KeyError: 'RNA-o'`

The traceback points to OpenMM while creating the system (`forcefield.createSystem()`).

I assume AF3 uses standard nomenclature for atoms and residues, so I was wondering whether this is a known issue with the force field used by ChimeraX for minimization, or if there is a way to work around it.

I am aware of the limitations of ChimeraX minimization and am only using it as a quick check before (eventually) proceeding with more rigorous refinement.

Thank you for any suggestions.

Best regards,
--
Bruno Hay Mele, PhD
https://github.com/bhym/

[1] metrics (pae/plddt/iptm) are very good
[2] just plain minimize #1
[3] Daily build of couple days ago (UCSF ChimeraX version: 1.13.dev202607062345 (2026-07-06)
)
<fold_s209a_model_0.cif>_______________________________________________
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