ValueError: Minimization failed after 100 attempts.

[looking-for-something]

AMBER relaxation: 86% 6/7 [elapsed: 28:31 remaining: 04:23] /usr/local/lib/python3.7/dist-packages/jax/_src/tree_util.py:201: FutureWarning: jax.tree_util.tree_multimap() is deprecated. Please use jax.tree_util.tree_map() instead as a drop-in replacement. 'instead as a drop-in replacement.', FutureWarning)

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.

ValueError: Minimization failed after 100 attempts.

[MWNautilus]

Something similar here: issue with AMBER relaxation step:

AMBER relaxation: 83%
5/6 [elapsed: 1:00:42 remaining: 11:07]

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

ValueError                                Traceback (most recent call last)

[<ipython-input-5-f89616eedc2d>](https://localhost:8080/#) in <module>()
     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](https://localhost:8080/#) 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.

-Michael.

[MWNautilus]

...the same task can be executed without any issues in ColabFold, incl. the AMBER relaxation steps: https://github.com/sokrypton/ColabFold

So, there is something selectively broken in the DeepMind Alphafold2 notebook, only. -Michael.

[Htomlinson14]

Closing as this duplicates https://github.com/deepmind/alphafold/issues/383