Docking stopped at it0 stage

HADDOCK
1

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

2

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.orghttp://bonvinlab.org
a.m.j.j.bonvin@uu.nlmailto:a.m.j.j.bonvin@uu.nl | T: +31 30 2533859

3

Dear Alexandre,

The cns1.3 was compiled by ifort.

Best
Changdong

4

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

5

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