# \[HADDOCK 3.0 local error\]: Symbol not found

**URL:** <https://ask.bioexcel.eu/t/haddock-3-0-local-error-symbol-not-found/4350>\
**Category:** HADDOCK\
**Created:** [May 25, 2023, 9:00pm UTC](https://ask.bioexcel.eu/t/haddock-3-0-local-error-symbol-not-found/4350 "2023-05-25T21:00:28Z")\
**Posts on this page:** 3\
**Page:** 1

<div class="post-metadata">

**Author:** ![zoeyxyang](https://avatars.discourse-cdn.com/v4/letter/z/91b2a8/32.png) [@zoeyxyang](https://ask.bioexcel.eu/u/zoeyxyang)\
**Post date:** [May 25, 2023, 9:00pm UTC](https://ask.bioexcel.eu/t/haddock-3-0-local-error-symbol-not-found/4350/1 "2023-05-25T21:00:28Z")

</div>

Hello,

I am running HADDOCK 3.0 locally for protein-protein docking.

I am running into an error and am wondering if you could point to me what this means.

In my log file, it seems like CNS ran okay, but something is wrong in the rigid body process:

> [2023-05-25 16:33:11,794 **init** INFO] [topoaa] Running CNS Jobs n=2
> 
> [2023-05-25 16:33:11,795 libmpi INFO] Executing tasks with the haddock3-mpitask runner using 48 processors…
> 
> [2023-05-25 16:33:27,068 **init** INFO] [topoaa] CNS jobs have finished
> 
> [2023-05-25 16:33:27,072 base\_cns\_module INFO] Module [topoaa] finished.
> 
> [2023-05-25 16:33:27,072 **init** INFO] [topoaa] took 15 seconds
> 
> [2023-05-25 16:33:28,229 base\_cns\_module INFO] Running [rigidbody] module
> 
> [2023-05-25 16:33:28,231 **init** INFO] [rigidbody] crossdock=true
> 
> [2023-05-25 16:33:28,231 **init** INFO] [rigidbody] Preparing jobs…
> 
> [2023-05-25 16:33:28,320 **init** INFO] [rigidbody] Running CNS Jobs n=10
> 
> [2023-05-25 16:33:28,321 libmpi INFO] Executing tasks with the haddock3-mpitask runner using 48 processors…
> 
> [2023-05-25 16:33:30,706 **init** INFO] [rigidbody] CNS jobs have finished
> 
> [2023-05-25 16:33:30,709 libutil ERROR] 100.00% of output was not generated for this module and tolerance was set to 0.00%.

I checked the output file in rigidbody\_1.out, and I saw this error:

> %NEXTCD-ERR: Symbol not found:  
> if ($mol\_fix\_origin\_$ncount  
> ^^^^^^^^^^^^^^^^^^^^^^^  
> MOMENTS  
> 907602.56366021-146489.24978483-298265.87224776  
> 283918.64291418 157029.31828698  
> 379726.61017238
> 
> MOMENTS  
> 73357.00623104 14542.39868540 -48724.59853486  
> 52519.65224370 -25884.46578269  
> 91056.91250709

Could you let me know what could be wrong?  
Thank you!

---

<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:** [May 25, 2023, 9:15pm UTC](https://ask.bioexcel.eu/t/haddock-3-0-local-error-symbol-not-found/4350/2 "2023-05-25T21:15:37Z")

</div>

Are there any PDB files written in the rigidbody dir or are they all failing?

When looking for errors, start from the bottom of the file.

Also make sure you are running the latest version as the code is evolving fast and we still do not have an official production release.

---

<div class="post-metadata">

**Author:** ![honoratorv](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/honoratorv/32/672_2.png) [@honoratorv](https://ask.bioexcel.eu/u/honoratorv)\
**Post date:** [May 26, 2023, 8:20am UTC](https://ask.bioexcel.eu/t/haddock-3-0-local-error-symbol-not-found/4350/3 "2023-05-26T08:20:33Z")

</div>

Thanks for reporting this issue.

Based on your logs it seems that no models were generated and `%NEXTCD-ERR: Symbol not found:` indicates an error at CNS level (the molecular engine used by Haddock). It has some fault tolerancy, meaning it can accumulate a few errors before it fails, so the actual cause or your issue can be a few (or maybe many) lines above.

To help us investigate the cause could you please share the full `rigidbody_1.out` file?