Hi Bruno,
I can reproduce this problem, and it happens for any RNA.  I have created a ticket (#20600 (Minimization of RNA fails)) with you as a recipient so that you will be notified when a fix is made.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab


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>_______________________________________________
ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu
To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu
Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/