ValueError: Minimization failed after 100 attempts.

[Belfield]

Hi,

Can anyone help with running AlphaFold Colab. We have run it many times before but recent;ly, and with the same protein sequences, the script returns the following error: ValueError: Minimization failed after 100 attempts.

Any help would be appreciated.

Thanks,

More details below:

---

ValueError Traceback (most recent call last)
in ()
88 max_outer_iterations=3,
89 use_gpu=True)
---> 90 relaxed_pdb, _, _ = amber_relaxer.process(prot=unrelaxed_proteins[best_model_name])
91 else:
92 print('Warning: Running without the relaxation stage.')

---

2 frames

---

/opt/conda/lib/python3.7/site-packages/alphafold/relax/amber_minimize.py in _run_one_iteration(pdb_string, max_iterations, tolerance, stiffness, restraint_set, max_attempts, use_gpu, exclude_residues)
417 logging.info(e)
418 if not minimized:
--> 419 raise ValueError(f"Minimization failed after {max_attempts} attempts.")
420 ret["opt_time"] = time.time() - start
421 ret["min_attempts"] = attempts

ValueError: Minimization failed after 100 attempts.

And when we try and submit the same job, we get this error message:

---

NotImplementedError Traceback (most recent call last)
in ()
19 with io.capture_output() as captured:
20 # Uninstall default Colab version of TF.
---> 21 get_ipython().magic('shell pip uninstall -y tensorflow')
22
23 get_ipython().magic('shell sudo apt install --quiet --yes hmmer')

3 frames
/usr/local/lib/python3.7/dist-packages/google/colab/_system_commands.py in _run_command(cmd, clear_streamed_output)
166 if locale_encoding != _ENCODING:
167 raise NotImplementedError(
--> 168 'A UTF-8 locale is required. Got {}'.format(locale_encoding))
169
170 parent_pty, child_pty = pty.openpty()

NotImplementedError: A UTF-8 locale is required. Got ANSI_X3.4-1968

[colaboratory-team]

Colab does not maintain the Alphafold notebooks, I would recommend reaching out to the Alphafold team via their github issue list. Your issue might be similar to this one