[HADDOCK 3.0 local error]: Symbol not found


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
283918.64291418 157029.31828698

73357.00623104 14542.39868540 -48724.59853486
52519.65224370 -25884.46578269

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

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.

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?