Rosetta FastRelax assert crash: Assertion res2.is_bonded(res1) failed with cyclic peptide-protein complex (multi-chain pose)

[kimlab-cnu]

Hello! I’m a graduate student in Korea studying protein design.

While adapting the supplementary code from “Accurate de novo design of high-affinity protein-binding macrocycles using deep learning” to work with Rosetta 2024 and PyRosetta 2024, I encountered a consistent crash during FastRelax:

Assertion res2.is_bonded(res1) failed

I reviewed related threads (e.g., #498) and PR #150 but I’m not fully sure how to apply that fix to my setup, or whether it is already included in the release I’m using.

### Environment

PyRosetta: 2024.39+release.59628fb
Rosetta: 2024.09+release.06b3cf8
OS: Rocky Linux (RHEL-compatible)
Run context: HPC cluster with Slurm

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I’m designing a target protein + cyclic peptide complex. I updated the XML and Python preprocessing based on the paper’s supplementary materials for 2024 versions of Rosetta/PyRosetta.

The run aborts with: Assertion res2.is_bonded(res1) failed.

I’m unsure whether #150’s changes are present in my release, or exactly how to apply them on my side if they are not.

Thank you very much for your time and any advice!