An error message after submitting docking

HADDOCK
1

Dear Haddock users,

Sorry for writing again but after submitting docking calculations I obtained new type of error:

Status: FAILED
There was an error in rigid body stage of the docking.

For more information, check the following CNS output files for error messages:
FAILED
complex_run1_it0_refine_1.out

In the output file:
Starting HADDOCK on: 2018-07-06 08:14:19

HADDOCK version: 2.2
Python version: 2.7.2 (default, Apr 4 2012, 13:50:40)
[GCC 4.1.2 20080704 (Red Hat 4.1.2-51)]
PYTHONPATH system variable contains:
[’/home/enmr/software/haddock2.2-grid/Haddock’, ‘/home/software/software/python2.7/lib/python2.7/site-packages/setuptools-0.9.8-py2.7.egg’, ‘/home/software/software/python2.7/lib/python2.7/site-packages/argparse-1.2.1-py2.7.egg’, ‘/home/software/software/python2.7/lib/python2.7/site-packages/recaptcha-1.0rc1-py2.7.egg’, ‘/home/enmr/services-enmr/HADDOCK2.2/server/run/userrun000245/run1’, ‘/home/software/software/modeller_v9.11/lib/x86_64-intel8’, ‘/home/software/software/modeller_v9.11/modlib’, ‘/home/software/software/numpy_stable/lib/python’, ‘/home/software/software/scipy/lib/python’, ‘/home/software/software/biopython/build/lib.linux-x86_64-2.7’, ‘/home/software/software/nose/lib/python’, ‘/home/enmr/services/HADDOCK/spyder’, ‘/home/software/software/moderna_source_1.7.1/build/lib’, ‘/home/software/software/cython/build/lib.linux-x86_64-2.7’, ‘/home/software/software/matplotlib/lib/python2.7/site-packages’, ‘/home/enmr/software/haddock2.2-grid’, ‘/home/software/software/python2.7/lib/python27.zip’, ‘/home/software/software/python2.7/lib/python2.7’, ‘/home/software/software/python2.7/lib/python2.7/plat-linux2’, ‘/home/software/software/python2.7/lib/python2.7/lib-tk’, ‘/home/software/software/python2.7/lib/python2.7/lib-old’, ‘/home/software/software/python2.7/lib/python2.7/lib-dynload’, ‘/home/software/software/python2.7/lib/python2.7/site-packages’]
parsing run.cns file
parsing new.html in /home/enmr/services-enmr/HADDOCK2.2/server/run/userrun000245/run1/data
reading parameters from the file /home/enmr/services-enmr/HADDOCK2.2/server/run/userrun000245/run1/data/new.html
setting some variables:
N_COMP set to: 2
RUN_NUMBER set to: 1
HADDOCK_DIR set to: /home/enmr/software/haddock2.2-grid
submit_save set to: Save updated parameters
PROT_SEGID_2 set to: B
PROT_SEGID_1 set to: A
PDB_FILE1 set to: protein1.pdb
AMBIG_TBL set to: ambig.tbl
PROJECT_DIR set to: /home/enmr/services-enmr/HADDOCK2.2/server/run/userrun000245
PDB_FILE2 set to: protein2.pdb
N_COMP 2
RUN_NUMBER 1
HADDOCK_DIR /home/enmr/software/haddock2.2-grid
submit_save Save updated parameters
PROT_SEGID_2 B
PROT_SEGID_1 A
PDB_FILE1 protein1.pdb
AMBIG_TBL ambig.tbl
PROJECT_DIR /home/enmr/services-enmr/HADDOCK2.2/server/run/userrun000245
PDB_FILE2 protein2.pdb
looking for existing files
waterdock false
generating PSF and PDB file of protein A with the command:
queue command:
/home/enmr/software/bin/ssub haddock complex_run1_generate_A.job
generating PSF and PDB file of protein B with the command:
queue command:
/home/enmr/software/bin/ssub haddock complex_run1_generate_B.job
waiting for the psf files…
29702582.milou.cm.cluster

29702583.milou.cm.cluster

merging topologies and coordinates files with the command:
queue command:
/home/enmr/software/bin/ssub haddock complex_run1_generate_complex.job
waiting for the merged files…
29702584.milou.cm.cluster

looking for iteration 0
working on iteration 0
starting DOCKING protocol
calculating structure 1
calculating structure 2
calculating structure 3
calculating structure 4
(…)
HADDOCK has detected an error
Check the FAILED file in /home/enmr/services-enmr/HADDOCK2.2/server/run/userrun000245/run1
Stopping…
##############################################################################
Finishing HADDOCK on: 2018-07-06 08:22:07
Au revoir.
Tot ziens.
Bye bye.

##############################################################################

Starting HADDOCK

N-components version of HADDOCK (current maximum is 6)

Copyright 2003-2015 Alexandre Bonvin, Utrecht University.

Originally adapted from Aria 1.2 from Nilges and Linge, EMBL.

All rights reserved.

This code is part of the HADDOCK software and governed by its

license. Please see the LICENSE file that should have been included

as part of this package.

##############################################################################

Starting HADDOCK on: 2018-07-06 08:22:07

HADDOCK version: 2.2
Python version: 2.7.2 (default, Apr 4 2012, 13:50:40)
[GCC 4.1.2 20080704 (Red Hat 4.1.2-51)]
PYTHONPATH system variable contains:
[’/home/enmr/software/haddock2.2-grid/Haddock’, ‘/home/software/software/python2.7/lib/python2.7/site-packages/setuptools-0.9.8-py2.7.egg’, ‘/home/software/software/python2.7/lib/python2.7/site-packages/argparse-1.2.1-py2.7.egg’, ‘/home/software/software/python2.7/lib/python2.7/site-packages/recaptcha-1.0rc1-py2.7.egg’, ‘/home/enmr/services-enmr/HADDOCK2.2/server/run/userrun000245/run1’, ‘/home/software/software/modeller_v9.11/lib/x86_64-intel8’, ‘/home/software/software/modeller_v9.11/modlib’, ‘/home/software/software/numpy_stable/lib/python’, ‘/home/software/software/scipy/lib/python’, ‘/home/software/software/biopython/build/lib.linux-x86_64-2.7’, ‘/home/software/software/nose/lib/python’, ‘/home/enmr/services/HADDOCK/spyder’, ‘/home/software/software/moderna_source_1.7.1/build/lib’, ‘/home/software/software/cython/build/lib.linux-x86_64-2.7’, ‘/home/software/software/matplotlib/lib/python2.7/site-packages’, ‘/home/enmr/software/haddock2.2-grid’, ‘/home/software/software/python2.7/lib/python27.zip’, ‘/home/software/software/python2.7/lib/python2.7’, ‘/home/software/software/python2.7/lib/python2.7/plat-linux2’, ‘/home/software/software/python2.7/lib/python2.7/lib-tk’, ‘/home/software/software/python2.7/lib/python2.7/lib-old’, ‘/home/software/software/python2.7/lib/python2.7/lib-dynload’, ‘/home/software/software/python2.7/lib/python2.7/site-packages’]
parsing run.cns file
parsing new.html in /home/enmr/services-enmr/HADDOCK2.2/server/run/userrun000245/run1/data
reading parameters from the file /home/enmr/services-enmr/HADDOCK2.2/server/run/userrun000245/run1/data/new.html
setting some variables:
N_COMP set to: 2
RUN_NUMBER set to: 1
HADDOCK_DIR set to: /home/enmr/software/haddock2.2-grid
submit_save set to: Save updated parameters
PROT_SEGID_2 set to: B
PROT_SEGID_1 set to: A
PDB_FILE1 set to: protein1.pdb
AMBIG_TBL set to: ambig.tbl
PROJECT_DIR set to: /home/enmr/services-enmr/HADDOCK2.2/server/run/userrun000245
PDB_FILE2 set to: protein2.pdb
N_COMP 2
RUN_NUMBER 1
HADDOCK_DIR /home/enmr/software/haddock2.2-grid
submit_save Save updated parameters
PROT_SEGID_2 B
PROT_SEGID_1 A
PDB_FILE1 protein1.pdb
AMBIG_TBL ambig.tbl
PROJECT_DIR /home/enmr/services-enmr/HADDOCK2.2/server/run/userrun000245
PDB_FILE2 protein2.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
HADDOCK has detected an error
Check the FAILED file in /home/enmr/services-enmr/HADDOCK2.2/server/run/userrun000245/run1
Stopping…
##############################################################################
Finishing HADDOCK on: 2018-07-06 08:22:07
Au revoir.
Tot ziens.
Bye bye.
Cleaning up HADDOCK run directory
Only files for structure #1 will be kept…

How to correct the error? Before submitting docking I used pdb_format.py tool to check my structures and everything was ok.

best
Urszula

2

Did you check that file? Start from the bottom and look for error messages.

Also did you look at the content of the FAILED file?

Most likely a problem with your restraints. If none are recognised the program will stop

3

I am not able to load or check the complex_run1_it0.out file under the FAILED I have TOTAL NUMBER OF DISTANCE RESTRAINTS FOR RIGID BODY DOCKING IS ZERO!
CONTROL YOUR PARAMETER SETTINGS AND RESTRAINT DEFINITIONS
STRUCTURE NUMBER 190
I have no idea what/where should I correct.

Urszula

4

The problem is with your distance restraints. Probably, you are providing ambig.tbl or unambig.tbl files and the definitions in those files are not correct. For example, if you have assi (segid A and resid 20) (segid B and resid 10) 2.0 2.0 0.0 but no residue 20 in segid A (first molecule), you will get this error if this is the only restraint you provided.

5

It thus all depends on how you defined your restraints

6

I am submitting the docking via haddock2 server and the only restrains are the active residues that I have to add. I am not providing any ambig.tbl or unambig.tbl files. Could I send you somehow my files, so that you could have a look at ?
best
Urszula

7

Yes send it to haddock.support@gmail.com

Make sure the active residue you define are present in the models you are submitting and don’t mix the first and second molecule