# 100.00% of output was not generated for this module and tolerance was set to 5.00%
**URL:** https://ask.bioexcel.eu/t/100-00-of-output-was-not-generated-for-this-module-and-tolerance-was-set-to-5-00/6202
**Category:** HADDOCK
**Created:** [July 21, 2026, 7:12am UTC](https://ask.bioexcel.eu/t/100-00-of-output-was-not-generated-for-this-module-and-tolerance-was-set-to-5-00/6202 "2026-07-21T07:12:57Z")
**Posts on this page:** 9
**Page:** 1
### Author:  [@Anupama1](https://ask.bioexcel.eu/u/Anupama1)
#### Post date: [July 21, 2026, 7:12am UTC](https://ask.bioexcel.eu/t/100-00-of-output-was-not-generated-for-this-module-and-tolerance-was-set-to-5-00/6202/1 "2026-07-21T07:12:57Z")
I am facing the error during protein peptide docking in haddock V3. My protein contains two domains defined as chainA and chainB. Both chains are reported to have functional role in ligand binding and activity. PDB file has been cleaned and prepared properly before docking using pdb-tools. Also similar cleaning and pdb file preparation was done for peptide using tools provided by haddock.
However, I keep ending up with error of “100.00% of output was not generated for this module and tolerance was set to 5.00%.”
I am new to haddock and finding it difficult to resolve the error.
Steps I have performed to solve the issue so far.
1. Checked the pdb format many times.
2. verified the \*.cfg file and also tried adding mol\_fix\_origin = false
3. added unambigious restraint file to define the segments of protein generated using command
haddock3-restraints restrain\_bodies pdbs/fixed\_apo\_rep100\_c0\_clean.pdb \> restraints/domain\_restraints.tbl
4. installed CNS library separately again cns\_v1.3\_r9, thinking this could be the source of error.
Error still persist with all the efforts.
---
### Author:  [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)
#### Post date: [July 21, 2026, 7:27am UTC](https://ask.bioexcel.eu/t/100-00-of-output-was-not-generated-for-this-module-and-tolerance-was-set-to-5-00/6202/2 "2026-07-21T07:27:25Z")
CNS should not be the issue.
To diagnose the problem, set in the general parameter header of the config file: debug=true
The output files will then be kept and you can check those in the rigidbody directory for error messages.
Are all files present and ok in the topoaa module?
Did you check / try to run some of the provided examples?
---
### Author:  [@Anupama1](https://ask.bioexcel.eu/u/Anupama1)
#### Post date: [July 22, 2026, 2:56am UTC](https://ask.bioexcel.eu/t/100-00-of-output-was-not-generated-for-this-module-and-tolerance-was-set-to-5-00/6202/3 "2026-07-22T02:56:59Z")
Thank you for your prompt response.
I checked all the files and they are present in the specified folder. They are correct, to the best of my understanding based on the available tutorials.
---
### Author:  [@Anupama1](https://ask.bioexcel.eu/u/Anupama1)
#### Post date: [July 22, 2026, 2:58am UTC](https://ask.bioexcel.eu/t/100-00-of-output-was-not-generated-for-this-module-and-tolerance-was-set-to-5-00/6202/4 "2026-07-22T02:58:15Z")
I did run the protein-peptide tutorial examples. They are running fine with no error.
---
### Author:  [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)
#### Post date: [July 22, 2026, 6:34am UTC](https://ask.bioexcel.eu/t/100-00-of-output-was-not-generated-for-this-module-and-tolerance-was-set-to-5-00/6202/5 "2026-07-22T06:34:49Z")
You still have most likely an issue either with your PDB files or the restraints.
Only way to help you is if you provide us all input data and your workflow.
Or set debug=true and rerun, then inspect the out files in the rigidbody directory for errors.
---
### Author:  [@Anupama1](https://ask.bioexcel.eu/u/Anupama1)
#### Post date: [July 22, 2026, 7:06am UTC](https://ask.bioexcel.eu/t/100-00-of-output-was-not-generated-for-this-module-and-tolerance-was-set-to-5-00/6202/6 "2026-07-22T07:06:08Z")
[rigidbody\_1.inp](https://ask.bioexcel.eu/uploads/short-url/5dyJmcD2CqxvWPO6aUPpY4lyzzQ.inp) (25.8 KB)
[domain\_restraints.tbl](https://ask.bioexcel.eu/uploads/short-url/7UoV79zICIpg2pUVMMv8TqO5pGF.tbl) (558 Bytes)
[Pep\_0001\_ambig.tbl](https://ask.bioexcel.eu/uploads/short-url/5IVP317YtKvUE5XctUbwGEGdzIr.tbl) (2.3 KB)
I am attaching the files for your reference
run\_dir = “runs/protein\_Pep\_0001”
mode = “local”
ncores = 20
debug = true
molecules = [
“pdbs/fixed\_apo\_rep100\_c0\_clean-fixed.pdb”,
“pdbs/Pep\_0001\_fix\_clean.pdb”
]
#### disables the automatic determination of histidine protonation state is set as false
[Pep\_0001\_fix\_clean.pdb](https://ask.bioexcel.eu/uploads/short-url/yRvghFig6tBKHd52sP7cAXhx5DV.pdb) (6.4 KB)
[fixed\_apo\_rep100\_c0\_clean-fixed.pdb](https://ask.bioexcel.eu/uploads/short-url/fUNwAfhi2vgcafkdFQq8IbOkzLZ.pdb) (1.1 MB)
[topoaa]
autohis = true
[rigidbody]
ambig\_fname = “restraints/Pep\_0001\_ambig.tbl”
#### Add inter-domain restraints here to keep Chains A and B together
unambig\_fname = “restraints/domain\_restraints.tbl”
sampling = 1000
[flexref]
tolerance = 5
ambig\_fname = “restraints/Pep\_0001\_ambig.tbl”
#### Add inter-domain restraints here to keep Chains A and B together
unambig\_fname = “restraints/domain\_restraints.tbl”
fle\_sta\_2 = 1
fle\_end\_2 = 5
fle\_seg\_2 = “C”
ssdihed = “alphabeta”
mdsteps\_cool1 = 2000
mdsteps\_cool2 = 4000
mdsteps\_cool3 = 4000
mdsteps\_rigid = 2000
[emref]
ambig\_fname = “restraints/Pep\_0001\_ambig.tbl”
#### Maintain restraints during final minimization
unambig\_fname = “restraints/domain\_restraints.tbl”
fle\_sta\_2 = 1
fle\_end\_2 = 5
fle\_seg\_2 = “C”
ssdihed = “alphabeta”
[seletop]
select = 200
[rmsdmatrix]
[clustrmsd]
clust\_cutoff= 5
plot\_matrix = true
[seletopclusts]
top\_models = 4
---
### Author:  [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)
#### Post date: [July 22, 2026, 9:54am UTC](https://ask.bioexcel.eu/t/100-00-of-output-was-not-generated-for-this-module-and-tolerance-was-set-to-5-00/6202/7 "2026-07-22T09:54:02Z")
Your receptor PDB file contains two chains.
For docking purposes an input PDB file should only contain a single chain.
So assign a single chainID to your protein, making sure there is not overlap in the numbering of residues.
---
### Author:  [@Anupama1](https://ask.bioexcel.eu/u/Anupama1)
#### Post date: [July 23, 2026, 1:59am UTC](https://ask.bioexcel.eu/t/100-00-of-output-was-not-generated-for-this-module-and-tolerance-was-set-to-5-00/6202/8 "2026-07-23T01:59:58Z")
Thank you for your response.
I will modify the pdb and submit the job accordingly.
However, I have question regarding haddock module. Currently it is not possible to dock multi chain protein in haddock?
Since in my case both chains are important for the binding and modulation of activity.
---
### Author:  [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)
#### Post date: [July 23, 2026, 6:25am UTC](https://ask.bioexcel.eu/t/100-00-of-output-was-not-generated-for-this-module-and-tolerance-was-set-to-5-00/6202/9 "2026-07-23T06:25:34Z")
You simply have to treat it as one chain - as is done for example for antibodies - check our online tutorials.
And you can dock more than two molecules, but the rule remains: one molecule - one chainID