%NEXTCD-ERR: Symbol not found

HADDOCK
1

Hello, everyone!
I ran the example provided and it worked.
Now I tried to dock a peptide to a protein. Both structures were provided in .pdb format, after I ran pdb_selaltloc.py. At the it0 step, I got this error:

  • Running parallel, 4 cores 1000 jobs
  • ERROR: Job rigid_body/complex_it0_000000.inp has failed, please check the output rigid_body/complex_it0_000000.out
    root@alex:/home/alex/share/haddock3-3.0.alpha2/examples/protein-protein# mc
    /home/alex/share/haddock3-3.0.alpha2/examples/protein-protein/run2/rigid_body/complex_it0_000000.out 608134/594K 100%
    CNSsolve> evaluate ($maxid = $ncount)
    CNSsolve> end if
    CNSsolve> end loop selectmol
    CNSsolve> display $maxid
    0
    CNSsolve> if ($Toppar.fix_origin_$maxid eq false) then
    %NEXTCD-ERR: Symbol not found:
    if ($Toppar.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: 2896298920 bytes
Maximum dynamic memory overhead: 2480 bytes
Program started at: 08:19:38 on 07-Oct-2020
Program stopped at: 08:19:38 on 07-Oct-2020
CPU time used: 0.5874 seconds
I have attached also the run1.toml file:
run1.txt (624 Bytes).
I am using HADDOCK-3.0-alpha.
Thank you in advance!
Kind regards,
Alexandru Tirziu

2

Thanks for your interest in HADDOCK3, but please keep in mind that this version is NOT to be used for production runs, only for development purposes.

If you are a developer and find a bug in the code, please open an issue in the public repository: https://github.com/haddocking/haddock3

This ALPHA version does NOT support Protein-Peptide docking, please use the default production version available both as a webserver and as standalone code:

3

I understand. Thank you!