Haddock3 example peptide-cyclisation

HADDOCK
1

I am trying to run the Haddock3 cyclic peptide example to test the system and to learn from it so i can work on my own peptides.
I have tried to run this example a couple of time but i am alaways stuck in the same place, the job is ending without creating any output, can you help me with understand the issue ere and how to solve it

Terminal output:
$ haddock3 run2-cyclise-3wne-full/data/configurations/raw_input.toml
[2025-08-11 16:11:11,843 defaults INFO] Using patched CNS path: /home/access/Desktop/Matan/cns_v1.3_r9/intel-x86_64bit-linux/bin/cns
[2025-08-11 16:11:13,355 cli INFO]
##############################################

HADDOCK3

##############################################

!! Some of the HADDOCK3 components use CNS (Crystallographic and NMR System) which is free of use for non-profit applications. !!
!! For commercial use it is your own responsibility to have a proper license. !!
!! For details refer to the DISCLAIMER file in the HADDOCK3 repository. !!

Starting HADDOCK3 v2025.7.1 on 2025-08-11 16:11:00

Python 3.9.13 | packaged by conda-forge | (main, May 27 2022, 16:56:21)
[GCC 10.3.0]

[2025-08-11 16:11:42,557 libworkflow INFO] Reading instructions step 0_topoaa
[2025-08-11 16:11:42,557 libworkflow INFO] Reading instructions step 1_flexref
[2025-08-11 16:11:42,559 libworkflow INFO] Reading instructions step 2_mdref
[2025-08-11 16:11:42,560 libworkflow INFO] Reading instructions step 3_caprieval
[2025-08-11 16:11:42,560 libworkflow INFO] Reading instructions step 4_rmsdmatrix
[2025-08-11 16:11:42,561 libworkflow INFO] Reading instructions step 5_clustrmsd
[2025-08-11 16:11:42,561 libworkflow INFO] Reading instructions step 6_seletopclusts
[2025-08-11 16:11:42,561 libworkflow INFO] Reading instructions step 7_caprieval
[2025-08-11 16:11:42,561 libworkflow INFO] Reading instructions step 8_topoaa
[2025-08-11 16:11:42,561 libworkflow INFO] Reading instructions step 9_emscoring
[2025-08-11 16:11:42,562 libworkflow INFO] Reading instructions step 10_flexref
[2025-08-11 16:11:42,563 libworkflow INFO] Reading instructions step 11_mdref
[2025-08-11 16:11:42,564 libworkflow INFO] Reading instructions step 12_caprieval
[2025-08-11 16:11:42,564 libworkflow INFO] Reading instructions step 13_rmsdmatrix
[2025-08-11 16:11:42,565 libworkflow INFO] Reading instructions step 14_clustrmsd
[2025-08-11 16:11:42,565 libworkflow INFO] Reading instructions step 15_seletopclusts
[2025-08-11 16:11:42,565 libworkflow INFO] Reading instructions step 16_caprieval
[2025-08-11 16:11:42,681 base_cns_module INFO] Running [topoaa] module
[2025-08-11 16:11:42,682 init INFO] [topoaa] Molecule 1: 3wne_peptide-ensemble.pdb
[2025-08-11 16:11:42,685 init INFO] [topoaa] Termini of molecule 1:
N-ter: uncharged C-ter: uncharged 5’phosphate: no
[2025-08-11 16:11:42,685 init INFO] [topoaa] Sanitizing molecule 3wne_peptide-ensemble_1.pdb
[2025-08-11 16:11:42,689 init INFO] [topoaa] Topology CNS input created
[2025-08-11 16:11:42,690 init INFO] [topoaa] Sanitizing molecule 3wne_peptide-ensemble_2.pdb
[2025-08-11 16:11:42,694 init INFO] [topoaa] Topology CNS input created
[2025-08-11 16:11:42,694 init INFO] [topoaa] Running CNS Jobs n=2
[2025-08-11 16:11:42,694 libutil INFO] Selected 2 cores to process 2 jobs, with 24 maximum available cores.
[2025-08-11 16:11:42,700 libparallel INFO] Using 2 cores
[2025-08-11 16:11:42,824 libparallel INFO] 2 tasks finished
[2025-08-11 16:11:42,825 init INFO] [topoaa] CNS jobs have finished
[2025-08-11 16:11:42,829 libutil ERROR] 100.00% of output was not generated for this module and tolerance was set to 0.00%.
Traceback (most recent call last):
File “/home/access/Desktop/Matan/haddock3/haddock-env/lib/python3.9/site-packages/haddock/libs/libutil.py”, line 378, in log_error_and_exit
yield
File “/home/access/Desktop/Matan/haddock3/haddock-env/lib/python3.9/site-packages/haddock/clis/cli.py”, line 193, in main
workflow.run()
File “/home/access/Desktop/Matan/haddock3/haddock-env/lib/python3.9/site-packages/haddock/libs/libworkflow.py”, line 43, in run
step.execute()
File “/home/access/Desktop/Matan/haddock3/haddock-env/lib/python3.9/site-packages/haddock/libs/libworkflow.py”, line 173, in execute
self.module.run() # type: ignore
File “/home/access/Desktop/Matan/haddock3/haddock-env/lib/python3.9/site-packages/haddock/modules/base_cns_module.py”, line 61, in run
self._run()
File “/home/access/Desktop/Matan/haddock3/haddock-env/lib/python3.9/site-packages/haddock/modules/topology/topoaa/init.py”, line 356, in _run
self.export_io_models(faulty_tolerance=self.params[“tolerance”])
File “/home/access/Desktop/Matan/haddock3/haddock-env/lib/python3.9/site-packages/haddock/modules/init.py”, line 309, in export_io_models
self.finish_with_error(_msg)
File “/home/access/Desktop/Matan/haddock3/haddock-env/lib/python3.9/site-packages/haddock/modules/init.py”, line 317, in finish_with_error
raise RuntimeError(reason)
RuntimeError: 100.00% of output was not generated for this module and tolerance was set to 0.00%.
[2025-08-11 16:11:42,831 libutil ERROR] 100.00% of output was not generated for this module and tolerance was set to 0.00%.
[2025-08-11 16:11:42,831 libutil ERROR] An error has occurred, see log file. And contact the developers if needed.
[2025-08-11 16:11:42,833 libutil INFO] Finished at 11/08/2025 16:11:42. For any help contact us at GitHub · Where software is built . Adiós! Tchau! Au revoir!.
(haddock-env)

2

Most likely an issue with the CNS executable

Check: https://github.com/haddocking/haddock3/blob/main/DEVELOPMENT.md and especially the troubleshooting the CNS executable section

If the CNS executable is working fine for your system, when calling it from the command line you should see something like:

============================================================
>                                                          >
>            Crystallography & NMR System (CNS)            |
>                         CNSsolve                         |
>                                                          >
============================================================
 Version: 1.3 at patch level U
 Status: Special UU release with Rg, paramagnetic
         and Z-restraints (A. Bonvin, UU 2013)
============================================================
3

I do see this message when calling the CNSin the command line, and i tried sevral different CNS.

4

Could you try replacing the CNS in the haddock installation by your version (instead of defining it in the config file)

also what is the content of the 0_topoaa directory?

5

Did you check that your installation is using the working executable?

And you are you running haddock? In local mode

6

I replace the CNS, and it seem to work fine.
the content of the 0_topoaa directory is :
3wne_peptide-ensemble_1.pdb 3wne_peptide-ensemble_2.pdb io.json params.cfg

7

Can you please alboorate about the “installation is using the working executable” part?
And yes i am working on local mode.

Still get the same issue:
$ haddock3 --restart 0 run2-cyclise-3wne-full/data/configurations/raw_input.toml
[2025-08-12 18:00:42,032 defaults INFO] Using patched CNS path: /home/access/Desktop/Matan/haddock3/haddock-env/lib/python3.9/site-packages/haddock/bin/cns_solve-1.31-UU-Linux-x86-glibc28.exe
[2025-08-12 18:00:43,412 cli INFO]
##############################################

HADDOCK3

##############################################

!! Some of the HADDOCK3 components use CNS (Crystallographic and NMR System) which is free of use for non-profit applications. !!
!! For commercial use it is your own responsibility to have a proper license. !!
!! For details refer to the DISCLAIMER file in the HADDOCK3 repository. !!

Starting HADDOCK3 v2025.7.1 on 2025-08-12 18:00:00

Python 3.9.13 | packaged by conda-forge | (main, May 27 2022, 16:56:21)
[GCC 10.3.0]

[2025-08-12 18:00:43,627 libutil WARNING] run2-cyclise-3wne-full_out/00_topoaa exists and it will be REMOVED!
[2025-08-12 18:00:43,629 libutil WARNING] run2-cyclise-3wne-full_out/01_topoaa exists and it will be REMOVED!
[2025-08-12 18:00:43,629 libutil WARNING] run2-cyclise-3wne-full_out/data/00_topoaa exists and it will be REMOVED!
[2025-08-12 18:00:43,630 libutil WARNING] run2-cyclise-3wne-full_out/data/02_flexref exists and it will be REMOVED!
[2025-08-12 18:00:43,630 libutil WARNING] run2-cyclise-3wne-full_out/data/03_mdref exists and it will be REMOVED!
[2025-08-12 18:00:43,630 libutil WARNING] run2-cyclise-3wne-full_out/data/04_caprieval exists and it will be REMOVED!
[2025-08-12 18:00:43,631 libutil WARNING] run2-cyclise-3wne-full_out/data/08_caprieval exists and it will be REMOVED!
[2025-08-12 18:00:43,631 libutil WARNING] run2-cyclise-3wne-full_out/data/11_flexref exists and it will be REMOVED!
[2025-08-12 18:00:43,631 libutil WARNING] run2-cyclise-3wne-full_out/data/13_caprieval exists and it will be REMOVED!
[2025-08-12 18:00:43,632 libutil WARNING] run2-cyclise-3wne-full_out/data/17_caprieval exists and it will be REMOVED!
[2025-08-12 18:00:43,632 prepare_run INFO] Uncompressing previous output files for folders:
[2025-08-12 18:01:09,240 libutil ERROR] The following parameters do not match any expected parameters for module ‘topoaa’:

  • ‘skip’ did you mean ‘cyclicpept’?.
    Traceback (most recent call last):
    File “/home/access/Desktop/Matan/haddock3/haddock-env/lib/python3.9/site-packages/haddock/libs/libutil.py”, line 378, in log_error_and_exit
    yield
    File “/home/access/Desktop/Matan/haddock3/haddock-env/lib/python3.9/site-packages/haddock/clis/cli.py”, line 151, in main
    params, other_params = setup_run(
    File “/home/access/Desktop/Matan/haddock3/haddock-env/lib/python3.9/site-packages/haddock/gear/prepare_run.py”, line 391, in setup_run
    validate_modules_params(modules_params, max_mols)
    File “/home/access/Desktop/Matan/haddock3/haddock-env/lib/python3.9/site-packages/haddock/gear/prepare_run.py”, line 159, in wrapper
    return func(*args, **kwargs)
    File “/home/access/Desktop/Matan/haddock3/haddock-env/lib/python3.9/site-packages/haddock/gear/prepare_run.py”, line 616, in validate_modules_params
    raise ConfigurationError(_msg)
    haddock.core.exceptions.ConfigurationError: The following parameters do not match any expected parameters for module ‘topoaa’:
  • ‘skip’ did you mean ‘cyclicpept’?.
    [2025-08-12 18:01:09,241 libutil ERROR] The following parameters do not match any expected parameters for module ‘topoaa’:
  • ‘skip’ did you mean ‘cyclicpept’?.
    [2025-08-12 18:01:09,241 libutil ERROR] An error has occurred, see log file. And contact the developers if needed.
    [2025-08-12 18:01:09,242 libutil INFO] Finished at 12/08/2025 18:01:09. For any help contact us at GitHub · Where software is built . Ciao! 再见! Do pobachennya!.
    (haddock-env)
8

from the current log file you have an error in your config file: skip is not a valid parameter