Local HADDOCK failed on Linux machine

Dear All,

I have already run successfully on my mac os x. I am trying to run the same job on Ubuntu linux machine. However, I receive the following error:

Starting HADDOCK on: 2021-02-01 02:14:42

HADDOCK version: 2.4 - January 2021 release
Python version: 2.7.18 (default, Aug 4 2020, 11:16:42)
[GCC 9.3.0]
parsing run.cns file
parsing run.param in /home/alireza_antiverse_io/haddock2.4-2021-01/project/run1/data
reading parameters from the file /home/alireza_antiverse_io/haddock2.4-2021-01/project/run1/data/run.param
setting some variables:
N_COMP set to: 2
RUN_NUMBER set to: 1
HADDOCK_DIR set to: /home/alireza_antiverse_io/haddock2.4-2021-01
UNAMBIG_TBL set to: antibody-antigen-unambig.tbl
PROT_SEGID_2 set to: B
PROT_SEGID_1 set to: A
PDB_FILE1 set to: 4g6k_clean.pdb
AMBIG_TBL set to: antibody-antigen-ambig.tbl
PROJECT_DIR set to: /home/alireza_antiverse_io/haddock2.4-2021-01/project
PDB_FILE2 set to: 4i1b.pdb
N_COMP 2
RUN_NUMBER 1
HADDOCK_DIR /home/alireza_antiverse_io/haddock2.4-2021-01
UNAMBIG_TBL antibody-antigen-unambig.tbl
PROT_SEGID_2 B
PROT_SEGID_1 A
PDB_FILE1 4g6k_clean.pdb
AMBIG_TBL antibody-antigen-ambig.tbl
PROJECT_DIR /home/alireza_antiverse_io/haddock2.4-2021-01/project
PDB_FILE2 4i1b.pdb
looking for existing files
waterdock false
waiting for the psf files…
looking for iteration 0
working on iteration 0
increased number of structures requested for it0
==> regenerating file.nam file.list and file.cns in begin directory
starting DOCKING protocol
FIX: Modifying random seed for it 0 structure 2
Waiting to restart job…

Structure 1: running
Structure 2: crashed
Structure 3: crashed
Structure 4: crashed
Structure 5: crashed
Structure 6: crashed
Structure 7: crashed
Structure 8: crashed
Structure 9: crashed
Structure 10: crashed

calculating structure 2
  queue command:
  /bin/csh project_run1_it0_refine_2.job

Structure 1: running
Structure 2: running
Structure 3: failed
Structure 4: failed
Structure 5: failed
Structure 6: failed
Structure 7: failed
Structure 8: failed
Structure 9: failed
Structure 10: failed

python: Command not found.


Structure 1: running
Structure 2: failed
Structure 3: failed
Structure 4: failed
Structure 5: failed
Structure 6: failed
Structure 7: failed
Structure 8: failed
Structure 9: failed
Structure 10: failed

Timeout - deleting: /home/alireza_antiverse_io/haddock2.4-2021-01/project/run1/project_run1_it0_refine_1.out
Time-out of structure 1
Restarting failed structures…


calculating structure 1
  queue command:
  /bin/csh project_run1_it0_refine_1.job

Structure 1: running
Structure 2: failed
Structure 3: failed
Structure 4: failed
Structure 5: failed
Structure 6: failed
Structure 7: failed
Structure 8: failed
Structure 9: failed
Structure 10: failed

python: Command not found.

HADDOCK cannot continue due to too many (>20%) failed structures in it0
The following structures could not be docked:
[1, 2, 3, 4, 5, 6, 7, 8, 9, 10]
##############################################################################
Finishing HADDOCK on: 2021-02-01 02:20:12
Au revoir.
Tot ziens.
Bye bye.

For some reason, HADDOCK fails to run the jobs. I could not figure out what “Python: command not found” meant. I use python2.7. I also see the PDB files in it0 directory.

Could you advise me why I get this error?

Thank you,

Alireza

What happens if in tcsh or csh you type python?

Is it found? If not, make sure it is in your path.

Thank you, Dr. Bonvin,

The problem was broken symlink for python. I linked python correctly, and that solved the problem.

Best regards,
Alireza