Minimization fails with notebook relax_amber.ipynb

Hi,

We are trying to use the only AMBER relax notebook and encountered an issue. Do you have any ideas why it could have happened?

Thank you!

Expected Behavior

Uploading a PDB file to relax_amber.ipynb and getting the relaxed structure

Current Behavior

After uploading, the minimization fails, with the error in the ColabFold output part.

Steps to Reproduce (for bugs)

we provided the PDB file that was used, just renamed it to .txt instead of .pdb
amber1.txt

ColabFold Output (for bugs)

amber1.pdb(application/x-aportisdoc) - 62226 bytes, last modified: n/a - 100% done

Saving amber1.pdb to amber1.pdb

---------------------------------------------------------------------------

ValueError                                Traceback (most recent call last)

[<ipython-input-3-6b2a34f498ab>](https://localhost:8080/#) in <module>
      6 from google.colab import files
      7 pdb_dict = files.upload()
----> 8 relax_me(pdb_in=list(pdb_dict.keys())[0],
      9          pdb_out="relaxed.pdb")
     10 files.download(f'relaxed.pdb')

3 frames

[/opt/conda/lib/python3.8/site-packages/alphafold/relax/amber_minimize.py](https://localhost:8080/#) in _run_one_iteration(pdb_string, max_iterations, tolerance, stiffness, restraint_set, max_attempts, use_gpu, exclude_residues)
    418       logging.info(e)
    419   if not minimized:
--> 420     raise ValueError(f"Minimization failed after {max_attempts} attempts.")
    421   ret["opt_time"] = time.time() - start
    422   ret["min_attempts"] = attempts

ValueError: Minimization failed after 100 attempts.

Context

We run AF2 locally but could not install AMBER, so we wanted to run relax_amber.ipynb

Your Environment

Colab

Start with relax_amber.ipynb and reproduce the failure in Colab using the attached amber1.txt file renamed to .pdb. Inspect the relax_me call and the AlphaFold amber_minimize.py traceback to determine why minimization fails after 100 attempts. Done means identifying the cause and confirming whether the notebook can produce the expected relaxed structure.