From the error it looks like maybe(?) something failed in the molecular dynamics.
The next thing I would do is to switch off the cleanup flag in the project rerun the calculation and look at the cns output.
Have a look in the directory tmp and find the most recent directory called aria_temp.@xxxxx
(where xxxx is some random set of letters and numbers)
there should be a series of
run directories one for each structure (run_cns_1 run_cns_2…)
inside each run_cns_xxx there
should be a file called refine.out
have a look in this and look
for something that says error, this should tell what error was encountered during the dynamics (though what it say maybe cryptic)
if you do find an error but
cant understand it send me the out file and I will try and read it
regards
Gary
This
is getting more appropriate for the aria mailing list
https://groups.yahoo.com/neo/groups/aria-discuss/info
but
from the traceback, it looks as if that example is set to use condor as the job manager (one of the HPC/GRID job managers). This is unlikely to be appropriate if you're just trying to run the calculations on your local machine or network.
My
current versions of ARIA (up to 2.3.2b) don't show the condor switch in the GUI, but maybe the grid one does. In any case, the ARIA project .xml file is not too scary to edit with a text editor.
Dr.
Brian O. Smith --------------------------- Brian Smith at glasgow ac uk
Institute
of Molecular, Cell and Systems Biology & School of Life Sciences,
College
of Medical, Veterinary & Life Sciences,
Joseph
Black Building, University of Glasgow, Glasgow G12 8QQ, UK.
Tel:
0141 330 5167/6459/3089
https://www.gla.ac.uk/researchinstitutes/biology/research/structuralbiologybiophysicalcharacterisationfacility/
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The
University of Glasgow, charity number SC004401
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From:
CcpNmr software mailing list [[log in to unmask]]
on behalf of Francisco Conejero-Lara [[log in to unmask]]
Sent:
08 May 2019 13:37
To: [log in to unmask]
Subject:
Re: Error running ARIA 2.3 with ccpn
Thank
you Brian. After installing the patches ARIA starts OK. I am testing the installation with an example project provided at ARIA site.
However,
it stops now during the first interation of the calculation with the following message:
MESSAGE
[CNS]: CNS output files have been copied to /Users/conejero/Aria/nilges/
example/tudor/run1/structures/it0/cns
MESSAGE
[Job manager]: shutdown.
Traceback
(most recent call last):
File
"/Applications/ccpnmr/aria2.3/aria2.py", line 903, in <module>
verbose_level,
use_condor=condor)
File
"/Applications/ccpnmr/aria2.3/aria2.py", line 813, in run_aria
project.go(use_condor)
File
"/Applications/ccpnmr/aria2.3/src/py/aria/Project.py", line 1666, in go
self.run_protocol(first_iteration)
File
"/Applications/ccpnmr/aria2.3/src/py/aria/Project.py", line 1672, in run_protocol
last_iteration
= self.getProtocol().go(iteration, self.getMolecule())
File
"/Applications/ccpnmr/aria2.3/src/py/aria/Protocol.py", line 1841, in go
iteration
= self.start(iteration, molecule)
File
"/Applications/ccpnmr/aria2.3/src/py/aria/Protocol.py", line 1825, in start
return
self.run_protocol(molecule, iteration)
File
"/Applications/ccpnmr/aria2.3/src/py/aria/Protocol.py", line 2300, in run_protocol
is_first_it)
File
"/Applications/ccpnmr/aria2.3/src/py/aria/Protocol.py", line 2255, in run_iteration
self.error(StandardError,
err_msg)
File
"/Applications/ccpnmr/aria2.3/src/py/aria/ariabase.py", line 211, in error
raise
exception, msg
StandardError:
USER ERROR <aria.Protocol.Protocol> File "/Applications/ccpnmr/aria2.3/src/py/aria/Protocol.py", line 2300 in run_protocol
Structure
calculation failed for structure 1.
Structure
calculation failed for structure 2.
Structure
calculation failed for structure 3.
Structure
calculation failed for structure 4.
Structure
calculation failed for structure 5.
Structure
calculation failed for structure 6.
Structure
calculation failed for structure 7.
Structure
calculation failed for structure 8.
Structure
calculation failed for structure 9.
Structure
calculation failed for structure 10.
Please
check your setup and the CNS output files for errors.
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