AlphaFold not working

[Alleko]

I've been running Alphafold without many problems for a few months. It stopped executing tasks even the ones it used to be able to. Could you please help? :

Last 6 days alhphafold kept giving the same error message despite whatever protein sequence I ran. As a control I ran simple protein sequences that alphafold was able to predict before. Now it cannot do even these controls. Could you please help? Below is the error.

0%| | 0/7 [elapsed: 00:00 remaining: ?] /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.')

[CameronWeller]

having the same issue

[tonycheng1688]

Yes, we also encountered the same issue. But when we use ColabFold (MMseqs2) in google, it has no problem.

[tonycheng1688]

Here is the error screen.

[GaoSpark]

I also encountered this problem, looking forward to someone can solve it.

[BruceKMil]

Same issue, too! Has the futurewarning arrived?

[GaoSpark]

adding a flag to disable the relaxation stage in step 5. Running with run_relax=False can solve this problemn temporarily.

[BruceKMil]

Thank you. Am trying that at the moment.

Regards, Bruce

On 31 Jul 2022, at 6:08 pm, GaoSpark @.***> wrote:

adding a flag to disable the relaxation stage in step 5. Running with run_relax=False can solve this problemn temporarily.

— Reply to this email directly, view it on GitHub https://github.com/deepmind/alphafold/issues/539#issuecomment-1200372401, or unsubscribe https://github.com/notifications/unsubscribe-auth/AWOLOXOR5KY4JE3GDSI5JNTVWYYADANCNFSM54IUFSMQ. You are receiving this because you commented.

Bruce Milthorpe @.***

[Htomlinson14]

Hi! Thanks so much for raising the issue. Closing this as there is a duplicate issue https://github.com/deepmind/alphafold/issues/383

[Alleko]

Dear Hamish, I wish all is well with you, I could not use Alphafold because of this bug for the last two months or so. We have been paying for the Pro subscription all along. Is there a way to really solve this issue? Alphafold is not running even with simplest proteins right now. I am wondering what is wrong since it used to work with these simple proteins and it stopped all for good. Thank you!

[Alleko]