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I0404 21:01:29.229502 140648689870656 amber_minimize.py:69] Restraining 478 / 979 particles.
I0404 21:01:29.413306 140648689870656 amber_minimize.py:418] Unit "kilocalorie/mole" is not compatible with Unit "kilojoule/(nanometer*mole)".
I0404 21:01:29.493218 140648689870656 amber_minimize.py:408] Minimizing protein, attempt 100 of 100.
I0404 21:01:29.597103 140648689870656 amber_minimize.py:69] Restraining 478 / 979 particles.
I0404 21:01:29.781777 140648689870656 amber_minimize.py:418] Unit "kilocalorie/mole" is not compatible with Unit "kilojoule/(nanometer*mole)".
Traceback (most recent call last):
File "/home/af2/alphafold_2.3.2/run_alphafold.py", line 570, in <module>
app.run(main)
File "/home/af2/miniconda3/envs/af_2.3.2/lib/python3.8/site-packages/absl/app.py", line 312, in run
_run_main(main, args)
File "/home/af2/miniconda3/envs/af_2.3.2/lib/python3.8/site-packages/absl/app.py", line 258, in _run_main
sys.exit(main(argv))
File "/home/af2/alphafold_2.3.2/run_alphafold.py", line 543, in main
predict_structure(
File "/home/af2/alphafold_2.3.2/run_alphafold.py", line 361, in predict_structure
relaxed_pdb_str, _, violations = amber_relaxer.process(
File "/home/af2/alphafold_2.3.2/alphafold/relax/relax.py", line 62, in process
out = amber_minimize.run_pipeline(
File "/home/af2/alphafold_2.3.2/alphafold/relax/amber_minimize.py", line 476, in run_pipeline
ret = _run_one_iteration(
File "/home/af2/alphafold_2.3.2/alphafold/relax/amber_minimize.py", line 420, in _run_one_iteration
raise ValueError(f"Minimization failed after {max_attempts} attempts.")
ValueError: Minimization failed after 100 attempts.
what could be a solution for this in alphafold 2.3.2 ?
Thanks
The text was updated successfully, but these errors were encountered:
I have the same issue. My feeling of the problem is openmm version. I have openmm 8.1.0 in my conda environment and the newest requirement of alphafold is 7.7.0. I tried to downgrade my openmm in conda but, for some reason, my conda would not let me downgrade. So I have not test this.
what could be a solution for this in alphafold 2.3.2 ?
Thanks
The text was updated successfully, but these errors were encountered: