# Rigid-body step fails with 100% output not generated (tolerance 5%) **URL:** \ **Category:** HADDOCK\ **Tags:** haddock, support, community\ **Created:** [September 16, 2025, 8:32pm UTC](https://ask.bioexcel.eu/t/rigid-body-step-fails-with-100-output-not-generated-tolerance-5/5889 "2025-09-16T20:32:00Z")\ **Posts on this page:** 17\ **Page:** 1
**Author:** ![Yashpawar](https://avatars.discourse-cdn.com/v4/letter/y/90db22/32.png) [@Yashpawar](https://ask.bioexcel.eu/u/Yashpawar)\ **Post date:** [September 16, 2025, 8:32pm UTC](https://ask.bioexcel.eu/t/rigid-body-step-fails-with-100-output-not-generated-tolerance-5/5889/1 "2025-09-16T20:32:00Z")
Hello everyone, I’m facing a significant issue with the HADDOCK3 rigid-body docking step. The process fails completely, and I receive the following error: RuntimeError: 100.00% of output was not generated for this module and tolerance was set to 5.00%. I am attempting to perform a flexible peptide docking of the 4dx5 protein with the CaNCR36 peptide. System & Setup Details HADDOCK3 Version: v2025.9.0 Operating System: Linux, Ubuntu 24.04 CPU Cores: 12 available, 6-10 used RAM: 8 GB Python Version: 3.9.23 CNS: Confirmed as installed for non-commercial use Command Run: haddock3 config.toml Troubleshooting Steps I’ve Taken I have already tried a number of common solutions, but none have resolved the issue: Reduced the number of cores used from 10 to 6. Checked my input PDB files (protein.pdb, peptide.pdb) in PyMOL for obvious steric clashes or broken chains. Temporarily increased the tolerance value in the config.toml file. Reduced the sampling size for the docking run. Verified that my CNS installation and licensing are correct and functional. ---
**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:** [September 16, 2025, 8:50pm UTC](https://ask.bioexcel.eu/t/rigid-body-step-fails-with-100-output-not-generated-tolerance-5/5889/2 "2025-09-16T20:50:04Z")
Can you run any of the examples provided? If this works fine, to further investigate you should set debug=true in the config file and check the out/err files in the rigidbody directory. Also did you try a simple: pip install haddock3 ? ---
**Author:** ![Yashpawar](https://avatars.discourse-cdn.com/v4/letter/y/90db22/32.png) [@Yashpawar](https://ask.bioexcel.eu/u/Yashpawar)\ **Post date:** [September 17, 2025, 12:41pm UTC](https://ask.bioexcel.eu/t/rigid-body-step-fails-with-100-output-not-generated-tolerance-5/5889/3 "2025-09-17T12:41:06Z")
Hi, Yes, I have **installed HADDOCK3 using `pip install haddock3`**. I also tried running one of the **example workflows provided with HADDOCK3** , and the example runs fine without errors. However, in my **protein-peptide docking case** : - `topoaa` runs successfully for both molecules. - `rigidbody` module executes CNS jobs, but **100% output is missing** , even with `debug=true`. I have checked the `out/err` files in the `rigidbody` directory, and the error persists. Could you please advise why the **rigid-body stage fails for my inputs** while the examples run fine? ---
**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:** [September 17, 2025, 4:14pm UTC](https://ask.bioexcel.eu/t/rigid-body-step-fails-with-100-output-not-generated-tolerance-5/5889/4 "2025-09-17T16:14:11Z")
Can you share the err/out files from the rigidbody directory? The answer must be in those files (at the end of the file most likely) ---
**Author:** ![Yashpawar](https://avatars.discourse-cdn.com/v4/letter/y/90db22/32.png) [@Yashpawar](https://ask.bioexcel.eu/u/Yashpawar)\ **Post date:** [September 17, 2025, 6:06pm UTC](https://ask.bioexcel.eu/t/rigid-body-step-fails-with-100-output-not-generated-tolerance-5/5889/5 "2025-09-17T18:06:11Z")
%NEXTCD-ERR: Symbol not found: if ($mol\_fix\_origin\_$maxid ^^^^^^^^^^^^^^^^^^^^^^ %NEXTCD-ERR: Symbol not found: if ($mol\_fix\_origin\_$maxid ^^^^^^^^^^^^^^^^^^^^^^ %NEXTCD-ERR: Symbol not found: if ($mol\_fix\_origin\_$maxid ^^^^^^^^^^^^^^^^^^^^^^ %NEXTCD-ERR: Symbol not found: if ($mol\_fix\_origin\_$maxid ^^^^^^^^^^^^^^^^^^^^^^ %NEXTCD-ERR: Symbol not found: if ($mol\_fix\_origin\_$maxid ^^^^^^^^^^^^^^^^^^^^^^ %NEXTCD-ERR: Symbol not found: if ($mol\_fix\_origin\_$maxid ^^^^^^^^^^^^^^^^^^^^^^ %NEXTCD-ERR: Symbol not found: if ($mol\_fix\_origin\_$maxid ^^^^^^^^^^^^^^^^^^^^^^ %NEXTCD-ERR: Symbol not found: if ($mol\_fix\_origin\_$maxid ^^^^^^^^^^^^^^^^^^^^^^ %NEXTCD-ERR: Symbol not found: if ($mol\_fix\_origin\_$maxid ^^^^^^^^^^^^^^^^^^^^^^ %PARSER error encountered: Encountered too many parsing errors. (CNS is in mode: SET ABORT=NORMal END) * * * ABORT mode will terminate program execution. * * * # Program will stop immediately. # Maximum dynamic memory allocation: 2892037280 bytes Maximum dynamic memory overhead: 1392 bytes Program started at: 18:58:03 on 17-Sep-2025 Program stopped at: 18:58:05 on 17-Sep-2025 CPU time used: 2.0086 seconds ---
**Author:** ![Yashpawar](https://avatars.discourse-cdn.com/v4/letter/y/90db22/32.png) [@Yashpawar](https://ask.bioexcel.eu/u/Yashpawar)\ **Post date:** [September 17, 2025, 6:10pm UTC](https://ask.bioexcel.eu/t/rigid-body-step-fails-with-100-output-not-generated-tolerance-5/5889/6 "2025-09-17T18:10:32Z")
this is my config file , ==================================================================== # HADDOCK3 Config – Protein-Peptide Docking # ==================================================================== # Global run parameters run\_dir = “run\_targeted” mode = “local” ncores = 8 debug = true # Input molecules molecules = [ “4dx5.pdb”, “CaNCR36.pdb” ] # -------------------------------------------------------------------- # Topology # -------------------------------------------------------------------- [topoaa] autohis = true delenph = true # -------------------------------------------------------------------- # Rigid-body docking # -------------------------------------------------------------------- [rigidbody] mol\_fix\_origin\_1 = true mol\_fix\_origin\_2 = false sampling = 10 tolerance = 20 ambig\_fname = “ambig.tbl” w\_vdw = 0.01 w\_elec = 1.0 w\_desolv = 1.0 w\_air = 0.1 debug = true # -------------------------------------------------------------------- # Select top rigid-body solutions # -------------------------------------------------------------------- [seletop] select = 2 # -------------------------------------------------------------------- # Flexible refinement # -------------------------------------------------------------------- [flexref] sampling\_factor = 2 tolerance = 5 mdsteps\_rigid = 200 mdsteps\_cool1 = 1000 mdsteps\_cool2 = 1000 mdsteps\_cool3 = 2000 # -------------------------------------------------------------------- # Energy minimization # -------------------------------------------------------------------- [emref] sampling\_factor = 2 tolerance = 5 nemsteps = 1000 # -------------------------------------------------------------------- # FCC Clustering # -------------------------------------------------------------------- [clustfcc] clust\_cutoff = 0.6 min\_population = 4 # -------------------------------------------------------------------- # CAPRI evaluation # -------------------------------------------------------------------- [caprieval] allatoms = true ---
**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:** [September 17, 2025, 7:48pm UTC](https://ask.bioexcel.eu/t/rigid-body-step-fails-with-100-output-not-generated-tolerance-5/5889/7 "2025-09-17T19:48:49Z")
Ok - you seem to have hit a bug actually (an unlikely one, but still a bug) For now if you were to set `mol_fix_origin_1 = false` it should run. ---
**Author:** ![Yashpawar](https://avatars.discourse-cdn.com/v4/letter/y/90db22/32.png) [@Yashpawar](https://ask.bioexcel.eu/u/Yashpawar)\ **Post date:** [September 17, 2025, 8:00pm UTC](https://ask.bioexcel.eu/t/rigid-body-step-fails-with-100-output-not-generated-tolerance-5/5889/8 "2025-09-17T20:00:00Z")
> [@amjjbonvin](#): > > Ok - you seem to have hit a bug actually (an unlikely one, but still a bug) Thanks for the suggestion. I tried setting `mol_fix_origin_1 = false` as you recommended, but unfortunately, the CNS script still fails with multiple `%NEXTCD-ERR: Symbol not found` errors, as I shared earlier. It seems like the underlying issue might be a bug in the CNS/HADDOCK template itself, possibly related to how `$mol_fix_origin_$ncount` is being expanded. Could you advise on any alternative workaround, or should we try updating the CNS templates / HADDOCK version? ---
**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:** [September 17, 2025, 8:05pm UTC](https://ask.bioexcel.eu/t/rigid-body-step-fails-with-100-output-not-generated-tolerance-5/5889/9 "2025-09-17T20:05:26Z")
I can’t reproduce the error by setting `mol_fix_origin_1 = true` in one of the examples. Can you share (e.g. via email) all your input data and the workflow script so that we can try to reproduce the error? ---
**Author:** ![Yashpawar](https://avatars.discourse-cdn.com/v4/letter/y/90db22/32.png) [@Yashpawar](https://ask.bioexcel.eu/u/Yashpawar)\ **Post date:** [September 17, 2025, 8:30pm UTC](https://ask.bioexcel.eu/t/rigid-body-step-fails-with-100-output-not-generated-tolerance-5/5889/10 "2025-09-17T20:30:32Z")
Can I get email id, so I will send you input data files ---
**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:** [September 18, 2025, 12:33pm UTC](https://ask.bioexcel.eu/t/rigid-body-step-fails-with-100-output-not-generated-tolerance-5/5889/11 "2025-09-18T12:33:07Z")
One possible cause of your problem is that each molecule provided to HADDOCK (in docking mode) should have a unique chainID. It could be that your protein contains multiple chains, which causes this strange problem. So check your input PDBs and make sure they contain a unique chain. For scoring scenarios this is not the case. ---
**Author:** ![Yashpawar](https://avatars.discourse-cdn.com/v4/letter/y/90db22/32.png) [@Yashpawar](https://ask.bioexcel.eu/u/Yashpawar)\ **Post date:** [September 21, 2025, 2:05pm UTC](https://ask.bioexcel.eu/t/rigid-body-step-fails-with-100-output-not-generated-tolerance-5/5889/12 "2025-09-21T14:05:31Z")
can you find out, what is the error ? i had share my input files my protein and receptor, restraint file and config file (Attachment CaNCR36\_4dx5.cfg is missing) > **(attachments)** > > [4dx5.pdb](https://ask.bioexcel.eu/uploads/short-url/lQqopfzpM0VQVgOki06NPEEUei2.pdb) (4.01 MB) > [CaNCR36.pdb](https://ask.bioexcel.eu/uploads/short-url/9tWRZTbYlTLmMGF8btMtmf0L67b.pdb) (24 KB) > [ambig.tbl](https://ask.bioexcel.eu/uploads/short-url/nlQ8myUGclurEbglcKiFEr96SZ4.tbl) (55.7 KB) ---
**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:** [September 21, 2025, 3:39pm UTC](https://ask.bioexcel.eu/t/rigid-body-step-fails-with-100-output-not-generated-tolerance-5/5889/13 "2025-09-21T15:39:30Z")
Simply check if each pdb you are providing has a unique chainID ---
**Author:** ![Yashpawar](https://avatars.discourse-cdn.com/v4/letter/y/90db22/32.png) [@Yashpawar](https://ask.bioexcel.eu/u/Yashpawar)\ **Post date:** [September 22, 2025, 5:00pm UTC](https://ask.bioexcel.eu/t/rigid-body-step-fails-with-100-output-not-generated-tolerance-5/5889/14 "2025-09-22T17:00:29Z")
yes 4dx5 have chain ID A,B,C,D and E and peptide have chain ID P ---
**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:** [September 22, 2025, 5:12pm UTC](https://ask.bioexcel.eu/t/rigid-body-step-fails-with-100-output-not-generated-tolerance-5/5889/15 "2025-09-22T17:12:17Z")
Then you will have to process your PDB to have a unique chain and non-overlapping numbering Check our online tutorial ---
**Author:** ![Yashpawar](https://avatars.discourse-cdn.com/v4/letter/y/90db22/32.png) [@Yashpawar](https://ask.bioexcel.eu/u/Yashpawar)\ **Post date:** [September 22, 2025, 5:46pm UTC](https://ask.bioexcel.eu/t/rigid-body-step-fails-with-100-output-not-generated-tolerance-5/5889/16 "2025-09-22T17:46:58Z")
Which haddock should I have to use ? Haddock2.4 or 3 ---
**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:** [September 22, 2025, 6:00pm UTC](https://ask.bioexcel.eu/t/rigid-body-step-fails-with-100-output-not-generated-tolerance-5/5889/17 "2025-09-22T18:00:26Z")
Doesn’t matter both will have the same requirements