# An error message after submitting docking **URL:** \ **Category:** HADDOCK\ **Created:** [July 6, 2018, 6:43am UTC](https://ask.bioexcel.eu/t/an-error-message-after-submitting-docking/1050 "2018-07-06T06:43:03Z")\ **Posts on this page:** 7\ **Page:** 1
**Author:** ![Urszula\_Uciechowska](https://avatars.discourse-cdn.com/v4/letter/u/ad7895/32.png) [@Urszula\_Uciechowska](https://ask.bioexcel.eu/u/Urszula_Uciechowska)\ **Post date:** [July 6, 2018, 6:43am UTC](https://ask.bioexcel.eu/t/an-error-message-after-submitting-docking/1050/1 "2018-07-06T06:43:03Z")
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 ---
**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:** [July 6, 2018, 7:10am UTC](https://ask.bioexcel.eu/t/an-error-message-after-submitting-docking/1050/2 "2018-07-06T07:10:22Z")
> [@Urszula\_Uciechowska](#): > > complex\_run1\_it0\_refine\_1.out 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 ---
**Author:** ![Urszula\_Uciechowska](https://avatars.discourse-cdn.com/v4/letter/u/ad7895/32.png) [@Urszula\_Uciechowska](https://ask.bioexcel.eu/u/Urszula_Uciechowska)\ **Post date:** [July 6, 2018, 8:57am UTC](https://ask.bioexcel.eu/t/an-error-message-after-submitting-docking/1050/3 "2018-07-06T08:57:46Z")
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 ---
**Author:** ![joaor](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/joaor/32/194_2.png) [@joaor](https://ask.bioexcel.eu/u/joaor)\ **Post date:** [July 6, 2018, 9:44am UTC](https://ask.bioexcel.eu/t/an-error-message-after-submitting-docking/1050/4 "2018-07-06T09:44:24Z")
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. ---
**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:** [July 6, 2018, 9:51am UTC](https://ask.bioexcel.eu/t/an-error-message-after-submitting-docking/1050/5 "2018-07-06T09:51:24Z")
It thus all depends on how you defined your restraints ---
**Author:** ![Urszula\_Uciechowska](https://avatars.discourse-cdn.com/v4/letter/u/ad7895/32.png) [@Urszula\_Uciechowska](https://ask.bioexcel.eu/u/Urszula_Uciechowska)\ **Post date:** [July 6, 2018, 10:30am UTC](https://ask.bioexcel.eu/t/an-error-message-after-submitting-docking/1050/6 "2018-07-06T10:30:49Z")
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 ---
**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:** [July 6, 2018, 10:52am UTC](https://ask.bioexcel.eu/t/an-error-message-after-submitting-docking/1050/7 "2018-07-06T10:52:47Z")
Yes send it to [haddock.support@gmail.com](mailto: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