# Haddock3 example peptide-cyclisation

**URL:** <https://ask.bioexcel.eu/t/haddock3-example-peptide-cyclisation/5861>\
**Category:** HADDOCK\
**Created:** [August 11, 2025, 1:17pm UTC](https://ask.bioexcel.eu/t/haddock3-example-peptide-cyclisation/5861 "2025-08-11T13:17:46Z")\
**Posts on this page:** 8\
**Page:** 1

<div class="post-metadata">

**Author:** ![MatanGabay](https://avatars.discourse-cdn.com/v4/letter/m/b5ac83/32.png) [@MatanGabay](https://ask.bioexcel.eu/u/MatanGabay)\
**Post date:** [August 11, 2025, 1:17pm UTC](https://ask.bioexcel.eu/t/haddock3-example-peptide-cyclisation/5861/1 "2025-08-11T13:17:47Z")

</div>

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](https://github.com/haddocking/haddock3/issues) . Adiós! Tchau! Au revoir!.  
(haddock-env)

---

<div class="post-metadata">

**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\
**Post date:** [August 11, 2025, 1:45pm UTC](https://ask.bioexcel.eu/t/haddock3-example-peptide-cyclisation/5861/2 "2025-08-11T13:45:40Z")

</div>

Most likely an issue with the CNS executable

Check: [https://github.com/haddocking/haddock3/blob/main/DEVELOPMENT.md](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:

```auto
============================================================
> >
> 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)
============================================================

```

---

<div class="post-metadata">

**Author:** ![MatanGabay](https://avatars.discourse-cdn.com/v4/letter/m/b5ac83/32.png) [@MatanGabay](https://ask.bioexcel.eu/u/MatanGabay)\
**Post date:** [August 11, 2025, 2:44pm UTC](https://ask.bioexcel.eu/t/haddock3-example-peptide-cyclisation/5861/3 "2025-08-11T14:44:43Z")

</div>

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

---

<div class="post-metadata">

**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\
**Post date:** [August 11, 2025, 3:24pm UTC](https://ask.bioexcel.eu/t/haddock3-example-peptide-cyclisation/5861/4 "2025-08-11T15:24:37Z")

</div>

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?

---

<div class="post-metadata">

**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\
**Post date:** [August 11, 2025, 5:22pm UTC](https://ask.bioexcel.eu/t/haddock3-example-peptide-cyclisation/5861/5 "2025-08-11T17:22:28Z")

</div>

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

And you are you running haddock? In local mode

---

<div class="post-metadata">

**Author:** ![MatanGabay](https://avatars.discourse-cdn.com/v4/letter/m/b5ac83/32.png) [@MatanGabay](https://ask.bioexcel.eu/u/MatanGabay)\
**Post date:** [August 12, 2025, 3:08pm UTC](https://ask.bioexcel.eu/t/haddock3-example-peptide-cyclisation/5861/6 "2025-08-12T15:08:21Z")

</div>

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

---

<div class="post-metadata">

**Author:** ![MatanGabay](https://avatars.discourse-cdn.com/v4/letter/m/b5ac83/32.png) [@MatanGabay](https://ask.bioexcel.eu/u/MatanGabay)\
**Post date:** [August 12, 2025, 3:11pm UTC](https://ask.bioexcel.eu/t/haddock3-example-peptide-cyclisation/5861/7 "2025-08-12T15:11:27Z")

</div>

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](https://github.com/haddocking/haddock3/issues) . Ciao! 再见! Do pobachennya!.  
(haddock-env)

---

<div class="post-metadata">

**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\
**Post date:** [August 12, 2025, 3:28pm UTC](https://ask.bioexcel.eu/t/haddock3-example-peptide-cyclisation/5861/8 "2025-08-12T15:28:39Z")

</div>

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