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haddocking
50.00% of output was not generated for this module and tolerance was set to 0.00%.
Describe the bug [2024-05-04 22:03:31,746 libutil ERROR] 50.00% of output was not generated for this module and tolerance was set to 0.00%.
To Reproduce Running with Config below:
====================================================================
Protein-ligand docking example
directory in which the scoring will be done
run_dir = "Nb17-ID3239"
execution mode
mode = "local" ncores = 40
in which queue the jobs should run, if nothing is defined
it will take the system's default
queue = "short"
concatenate models inside each job, concat = 5 each .job will produce 5 models
concat = 5
Limit the number of concurrent submissions to the queue
queue_limit = 100
molecules to be docked
molecules = [ "data/6vxf_ABCG2.pdb", "data/CycPeptMPDB_ID_3239_ChainB.pdb" ]
====================================================================
[topoaa] autohis = true ligand_param_fname = "data/ligand-prodrg.param" ligand_top_fname = "data/ligand-prodrg.top" delenph = false
[rigidbody] tolerance = 5 ambig_fname = "data/ambig-active-rigidbody.tbl" ligand_param_fname = "data/ligand-prodrg.param" ligand_top_fname = "data/ligand-prodrg.top" sampling = 20 w_vdw = 1.0
[caprieval]
[seletop] select = 200
[caprieval]
[flexref] tolerance = 5 ambig_fname = "data/ambig-passive.tbl" ligand_param_fname = "data/ligand-prodrg.param" ligand_top_fname = "data/ligand-prodrg.top" mdsteps_rigid = 0 mdsteps_cool1 = 0
[caprieval]
[rmsdmatrix] resdic_A = [247,248,249,250,251,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,] resdic_B = [ 1 ]
[clustrmsd] criterion = 'maxclust' n_clusters = 4 # the number of clusters to be formed
[seletopclusts] top_models = 4
[caprieval]
====================================================================
Expected behavior A clear and concise description of what you expected to happen.
Configuration (optional - remove if not relevant)
- OS:CentOS
It’s not a bug - most likely bad quality of your staring models - or a problem with the ligand param/topo files
These are required if you want to dock some other ligands and should be provided to haddock
Our haddock2.4 server generate those automatically. The standalone version does not
Thank you so much for answering, but I have 5000 samples to deal with, so I can't rely on the server. How can I generate the .top and .param files in large scales?
Some tips can be found at:
https://www.bonvinlab.org/software/haddock2.4/faq/#small-ligand-docking-with-haddock HADDOCK2.4 manual - Frequently Asked Questions bonvinlab.org
Further you could check the BioExcel BioBB modules. There is one to generate CNS topo/param file using acepype
Check: https://github.com/bioexcel/biobb_wf_ligand_parameterization (look for the CNS parametrisation tutorial)
I've used acpype to generate .top and .par files in CNS standards, but the same error repeated. When I force the topoaa step tolerance = 99, no models to dock for rigidbody step.
Check the out files in the 00_topoaa directory for error messages, starting from the end of the file
Did you define the correct file names in the config file? And your ligand should have a chainID defined in the PDB file
Error message be like this:
File "/public/home/acosdmq0yn/haddock3/src/haddock/modules/sampling/rigidbody/init.py", line 79, in _run sampling_factor = int(self.params["sampling"] / len(models_to_dock)) ZeroDivisionError: division by zero [2024-05-11 01:18:59,632 libutil ERROR] division by zero
Config file names have been corrected, and ligand chain ID have been defined and used in the .tbl file.
can you provide us with some more details? are you trying to dock a ligand to a protein? when you see this message after the topoaa module it typically means that something is wrong with one of your input structures
Starting HADDOCK 3.0.0 on 2024-08-09 17:57:00
Python 3.9.19 (main, Jul 23 2024, 07:17:30)
[GCC 10.2.1 20210110]
[2024-08-09 17:57:40,698 libworkflow INFO] Reading instructions step 0_topoaa
[2024-08-09 17:57:40,698 libworkflow INFO] Reading instructions step 1_rigidbody
[2024-08-09 17:57:40,698 libworkflow INFO] Reading instructions step 2_seletop
[2024-08-09 17:57:40,698 libworkflow INFO] Reading instructions step 3_flexref
[2024-08-09 17:57:40,699 libworkflow INFO] Reading instructions step 4_emref
[2024-08-09 17:57:40,699 libworkflow INFO] Reading instructions step 5_clustfcc
[2024-08-09 17:57:40,699 libworkflow INFO] Reading instructions step 6_seletopclusts
[2024-08-09 17:57:40,720 base_cns_module INFO] Running [topoaa] module
[2024-08-09 17:57:40,720 __init__ INFO] [topoaa] Molecule 1: fixed_H5_1.pdb
[2024-08-09 17:57:40,722 __init__ INFO] [topoaa] Sanitizing molecule fixed_H5_1.pdb
[2024-08-09 17:57:40,729 __init__ INFO] [topoaa] Topology CNS input created in fixed_H5_1.inp
[2024-08-09 17:57:40,729 __init__ INFO] [topoaa] Molecule 2: fixed_IL4R_structure.pdb
[2024-08-09 17:57:40,732 __init__ INFO] [topoaa] Sanitizing molecule fixed_IL4R_structure.pdb
[2024-08-09 17:57:40,750 __init__ INFO] [topoaa] Topology CNS input created in fixed_IL4R_structure.inp
[2024-08-09 17:57:40,750 __init__ INFO] [topoaa] Running CNS Jobs n=2
[2024-08-09 17:57:40,750 libutil INFO] Selected 2 cores to process 2 jobs, with 48 maximum available cores.
[2024-08-09 17:57:40,750 libparallel INFO] Using 2 cores
[2024-08-09 17:57:41,547 libparallel INFO] >> completed 50%
[2024-08-09 17:57:43,526 libparallel INFO] >> completed 100%
[2024-08-09 17:57:43,526 libparallel INFO] 2 tasks finished
[2024-08-09 17:57:43,526 __init__ INFO] [topoaa] CNS jobs have finished
[2024-08-09 17:57:43,528 base_cns_module INFO] Module [topoaa] finished.
[2024-08-09 17:57:43,528 __init__ INFO] [topoaa] took 3 seconds
[2024-08-09 17:57:44,113 base_cns_module INFO] Running [rigidbody] module
[2024-08-09 17:57:44,114 __init__ INFO] [rigidbody] crossdock=true
[2024-08-09 17:57:44,114 __init__ INFO] [rigidbody] Preparing jobs...
[2024-08-09 17:57:44,351 __init__ INFO] [rigidbody] Running CNS Jobs n=60
[2024-08-09 17:57:44,351 libutil INFO] Selected 4 cores to process 60 jobs, with 48 maximum available cores.
[2024-08-09 17:57:44,351 libparallel INFO] Using 4 cores
[2024-08-09 17:57:45,972 libparallel INFO] >> completed 10%
[2024-08-09 17:57:45,972 libparallel INFO] >> completed 20%
[2024-08-09 17:57:46,386 libparallel INFO] >> completed 30%
[2024-08-09 17:57:46,386 libparallel INFO] >> completed 40%
[2024-08-09 17:57:46,386 libparallel INFO] >> completed 50%
[2024-08-09 17:57:46,386 libparallel INFO] >> completed 60%
[2024-08-09 17:57:46,386 libparallel INFO] >> completed 70%
[2024-08-09 17:57:46,386 libparallel INFO] >> completed 80%
[2024-08-09 17:57:46,386 libparallel INFO] >> completed 90%
[2024-08-09 17:57:46,386 libparallel INFO] >> completed 100%
[2024-08-09 17:57:46,386 libparallel INFO] 60 tasks finished
[2024-08-09 17:57:46,386 __init__ INFO] [rigidbody] CNS jobs have finished
[2024-08-09 17:57:46,408 libutil ERROR] 100.00% of output was not generated for this module and tolerance was set to 50.00%.
Traceback (most recent call last):
File "/software/haddock3/src/haddock/libs/libutil.py", line 335, in log_error_and_exit
yield
File "/software/haddock3/src/haddock/clis/cli.py", line 185, in main
workflow.run()
File "/software/haddock3/src/haddock/libs/libworkflow.py", line 43, in run
step.execute()
File "/software/haddock3/src/haddock/libs/libworkflow.py", line 155, in execute
self.module.run() # type: ignore
File "/software/haddock3/src/haddock/modules/base_cns_module.py", line 61, in run
self._run()
File "/software/haddock3/src/haddock/modules/sampling/rigidbody/__init__.py", line 159, in _run
self.export_io_models(faulty_tolerance=self.params["tolerance"])
File "/software/haddock3/src/haddock/modules/__init__.py", line 291, in export_io_models
self.finish_with_error(_msg)
File "/software/haddock3/src/haddock/modules/__init__.py", line 300, in finish_with_error
raise RuntimeError(reason)
RuntimeError: 100.00% of output was not generated for this module and tolerance was set to 50.00%.
[2024-08-09 17:57:46,409 libutil ERROR] 100.00% of output was not generated for this module and tolerance was set to 50.00%.
[2024-08-09 17:57:46,409 libutil ERROR] An error has occurred, see log file. And contact the developers if needed.
[2024-08-09 17:57:46,409 libutil INFO] Finished at 09/08/2024 17:57:46. For any help contact us at https://github.com/haddocking/haddock3/issues. Agur! Good bye! Dovidenia!.
This is the log file I got. I got a problem that was in the issue at first, so I modified the pdb file through pdbFixer and ran haddock in my container again, and I got this error message. How do I fix it?
Check one of the output file in the rigidbody directory of the run. Look for error messages starting at the bottom of the file