# Run.cns-conf file generated instead of run.cns

**URL:** <https://ask.bioexcel.eu/t/run-cns-conf-file-generated-instead-of-run-cns/5358>\
**Category:** HADDOCK\
**Tags:** haddock\
**Created:** [December 6, 2024, 8:09am UTC](https://ask.bioexcel.eu/t/run-cns-conf-file-generated-instead-of-run-cns/5358 "2024-12-06T08:09:02Z")\
**Posts on this page:** 2\
**Page:** 1

<div class="post-metadata">

**Author:** ![valerio](https://avatars.discourse-cdn.com/v4/letter/v/3be4f8/32.png) [@valerio](https://ask.bioexcel.eu/u/valerio)\
**Post date:** [December 6, 2024, 8:09am UTC](https://ask.bioexcel.eu/t/run-cns-conf-file-generated-instead-of-run-cns/5358/1 "2024-12-06T08:09:02Z")

</div>

Dear Responsible,

I have set an Ab-antigen docking and when I execute haddock2.4 I get this error:

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

# 

# Starting HADDOCK2.4

# 

# N-components version of HADDOCK (current maximum is 20)

# 

# Copyright 2003-2020 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: 2024-12-06 09:05:16

HADDOCK version: 2.4 - March 2024  
Python version: 2.7.18 |Anaconda, Inc.| (default, Jun 4 2021, 14:47:46)  
[GCC 7.3.0]  
reading parameters from the file ./run.param  
setting some variables:  
N\_COMP set to: 2  
RUN\_NUMBER set to: 1  
HADDOCK\_DIR set to: /gporq3/store\_3/project/match/software/haddock2.4-2024-03  
UNAMBIG\_TBL set to: PROVA-TOTAL\_unambig.tbl  
PROT\_SEGID\_2 set to: B  
PROT\_SEGID\_1 set to: A  
PDB\_FILE1 set to: ./PROVA-TOTAL\_haddock.pdb  
AMBIG\_TBL set to: ./antibody-antigen-ambig.tbl  
PROJECT\_DIR set to: .  
PDB\_FILE2 set to: ./BLX.pdb  
runDir= ./run1  
project . exists, run 1 does not exist  
create the new run 1  
./PROVA-TOTAL\_haddock.pdb copied to ./run1/data/sequence after removing the chain and segIDs  
./BLX.pdb copied to ./run1/data/sequence after removing the chain and segIDs  
editing run.cns: setting the default values  
Traceback (most recent call last):  
File “/gporq3/store\_3/project/match/software/haddock2.4-2024-03//Haddock/RunHaddock.py”, line 155, in   
new[‘CRYO-EM\_FILE’],  
File “/gporq3/store\_3/project/match/software/haddock2.4-2024-03/Haddock/Main/Setup.py”, line 341, in SetupNewProject  
runcnshandle = TextFile.TextFile(runcnsfile)  
File “/gporq3/store\_3/project/match/software/haddock2.4-2024-03/Haddock/ThirdParty/TextFile.py”, line 29, in **init**  
raise IOError, (2, 'No such file or directory: ’ + filename)  
IOError: [Errno 2] No such file or directory: /gporq3/store\_3/project/match/software/haddock2.4-2024-03/protocols/run.cns  
Exception AttributeError: “TextFile instance has no attribute ‘file’” in \<bound method TextFile. **del** of \<Haddock.ThirdParty.TextFile.TextFile instance at 0x2b14ad14a730\>\> ignored

I have checked in the run1/protocols folder and I find a run.cns-conf file. I though I might rename it to run.cns but following haddock2.4 run would complain about the pre-existance of run1 folder.

Thanks for your help,

Valerio

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<div class="post-metadata">

**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:** [December 6, 2024, 2:07pm UTC](https://ask.bioexcel.eu/t/run-cns-conf-file-generated-instead-of-run-cns/5358/2 "2024-12-06T14:07:25Z")

</div>

looks like you did not configure properly your haddock installation. Check carefully the installation instructions