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No template found for CYS residue. #1093

@Farah-Nazir

Description

@Farah-Nazir

I0919 05:22:53.492983 139995525330752 amber_minimize.py:408] Minimizing protein, attempt 95 of 100.
I0919 05:22:54.197038 139995525330752 amber_minimize.py:418] No template found for residue 106 (CYS). The set of atoms matches CYM, but the bonds are different.
I0919 05:22:54.198706 139995525330752 amber_minimize.py:408] Minimizing protein, attempt 96 of 100.
I0919 05:22:54.902250 139995525330752 amber_minimize.py:418] No template found for residue 106 (CYS). The set of atoms matches CYM, but the bonds are different.
I0919 05:22:54.903900 139995525330752 amber_minimize.py:408] Minimizing protein, attempt 97 of 100.
I0919 05:22:55.607558 139995525330752 amber_minimize.py:418] No template found for residue 106 (CYS). The set of atoms matches CYM, but the bonds are different.
I0919 05:22:55.609225 139995525330752 amber_minimize.py:408] Minimizing protein, attempt 98 of 100.
I0919 05:22:56.312941 139995525330752 amber_minimize.py:418] No template found for residue 106 (CYS). The set of atoms matches CYM, but the bonds are different.
I0919 05:22:56.314572 139995525330752 amber_minimize.py:408] Minimizing protein, attempt 99 of 100.
I0919 05:22:57.018080 139995525330752 amber_minimize.py:418] No template found for residue 106 (CYS). The set of atoms matches CYM, but the bonds are different.
I0919 05:22:57.019768 139995525330752 amber_minimize.py:408] Minimizing protein, attempt 100 of 100.
I0919 05:22:57.723667 139995525330752 amber_minimize.py:418] No template found for residue 106 (CYS). The set of atoms matches CYM, but the bonds are different.
Traceback (most recent call last):
File "/home/data/alphafold-2.3.1/run_alphafold.py", line 432, in
app.run(main)
File "/home/data/.conda/envs/AF2/lib/python3.8/site-packages/absl/app.py", line 312, in run
_run_main(main, args)
File "/home/data/.conda/envs/AF2/lib/python3.8/site-packages/absl/app.py", line 258, in _run_main
sys.exit(main(argv))
File "/home/data/alphafold-2.3.1/run_alphafold.py", line 408, in main
predict_structure(
File "/home/data/alphafold-2.3.1/run_alphafold.py", line 243, in predict_structure
relaxed_pdb_str, _, violations = amber_relaxer.process(
File "/home/data/alphafold-2.3.1/alphafold/relax/relax.py", line 62, in process
out = amber_minimize.run_pipeline(
File "/home/data/alphafold-2.3.1/alphafold/relax/amber_minimize.py", line 476, in run_pipeline
ret = _run_one_iteration(
File "/home/data/alphafold-2.3.1/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.

Can someone please guide me, how to solve this?

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