# Docking stopped at it0 stage

**URL:** <https://ask.bioexcel.eu/t/docking-stopped-at-it0-stage/94>\
**Category:** HADDOCK\
**Created:** [May 18, 2016, 9:42am UTC](https://ask.bioexcel.eu/t/docking-stopped-at-it0-stage/94 "2016-05-18T09:42:47Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![LIU](https://avatars.discourse-cdn.com/v4/letter/l/a88e57/32.png) [@LIU](https://ask.bioexcel.eu/u/LIU)\
**Post date:** [May 18, 2016, 9:42am UTC](https://ask.bioexcel.eu/t/docking-stopped-at-it0-stage/94/1 "2016-05-18T09:42:48Z")

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Dear HADDOCK users,

I did protein-dna docking by haddock2.2 in local installation.

If the semi-flexible segments of protein and dna were both set to automated mode, the docking stopped when calculating structure 1 and gave the messages below.

I’ve checked the out file in /tmp directory, there are no error messages reported and all the things in begin directory are ok.

If the semi-flexible segments of protein and dna were NOT set to automated mode, docking runs smoothly.

Any idea about that?  
Thanks.

Best  
Changdong

## looking for iteration 0 working on iteration 0 starting DOCKING protocol calculating structure 1 queue command: ------------------------------------------------------------ csh orc6\_dna\_haddock2.2\_run1\_it0\_refine\_1.job Structure 1: running

[1] 17447  
[1] + Killed python protocols/KeepAlive.py orc6\_dna\_haddock2.2\_run1\_it0\_refine\_1.out  
forrtl: No space left on device  
forrtl: severe (38): error during write, unit 6, file /proc/17450/fd/1  
Image PC Routine Line Source  
cns1 000000000092FE39 Unknown Unknown Unknown  
cns1 000000000097583F Unknown Unknown Unknown  
cns1 0000000000972FC3 Unknown Unknown Unknown  
cns1 0000000000611C30 Unknown Unknown Unknown  
cns1 0000000000608D9C Unknown Unknown Unknown  
cns1 000000000043CBBF Unknown Unknown Unknown  
cns1 0000000000402F9E Unknown Unknown Unknown  
libc.so.6 00002AFFAAEDCEC5 Unknown Unknown Unknown  
cns1 0000000000402EA9 Unknown Unknown Unknown

gzip: /tmp/3c9a9470-6d3b-4577-81f8-e476fb052131/orc6\_dna\_haddock2.2\_run1\_it0\_refine\_1.out.gz: No space left on device  
Traceback (most recent call last):  
File “protocols/RemoveBadPDB.py”, line 30, in   
os.remove(pdbfile0)  
OSError: [Errno 2] No such file or directory: ‘structures/it0/orc6\_dna\_haddock2.2\_1.pdb0’  
mv: cannot stat ‘/tmp/3c9a9470-6d3b-4577-81f8-e476fb052131/orc6\_dna\_haddock2.2\_run1\_it0\_refine\_1.out.gz’: No such file or directory

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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:** [May 18, 2016, 9:59am UTC](https://ask.bioexcel.eu/t/docking-stopped-at-it0-stage/94/2 "2016-05-18T09:59:56Z")

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Two problems it seems:

1. Your cns exec gives errors… How did you compile it?

2. no space left on your tmp partition

Prof. A.M.J.J. Bonvin | Faculty of Science  
Utrecht University | [bonvinlab.org](http://bonvinlab.org)[http://bonvinlab.org](http://bonvinlab.org)  
a.m.j.j.bonvin@uu.nl[mailto:a.m.j.j.bonvin@uu.nl](mailto:a.m.j.j.bonvin@uu.nl) | T: +31 30 2533859

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<div class="post-metadata">

**Author:** ![LIU](https://avatars.discourse-cdn.com/v4/letter/l/a88e57/32.png) [@LIU](https://ask.bioexcel.eu/u/LIU)\
**Post date:** [May 18, 2016, 11:11am UTC](https://ask.bioexcel.eu/t/docking-stopped-at-it0-stage/94/3 "2016-05-18T11:11:12Z")

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Dear Alexandre,

The cns1.3 was compiled by ifort.

Best  
Changdong

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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:** [May 23, 2016, 12:52pm UTC](https://ask.bioexcel.eu/t/docking-stopped-at-it0-stage/94/4 "2016-05-23T12:52:17Z")

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What about the error message that your /tmp partition is full? How much space do you have in /tmp?

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<div class="post-metadata">

**Author:** ![LIU](https://avatars.discourse-cdn.com/v4/letter/l/a88e57/32.png) [@LIU](https://ask.bioexcel.eu/u/LIU)\
**Post date:** [June 23, 2016, 9:48am UTC](https://ask.bioexcel.eu/t/docking-stopped-at-it0-stage/94/5 "2016-06-23T09:48:28Z")

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> [@LIU](#):
>
> If the semi-flexible segments of protein and dna were both set to automated mode

Dear Alexandre,

Sorry for late reply.

Finally, the docking run successfully in which the semi-flexible segments of protein and dna were not set to automated mode.

Best  
Changdong