Discussion group for the ARIA software

[Xiao Wang <xiao.wang AT etu.parisdescartes.fr>]

Hi, Julien

I have met this. Remove any previous psf and template in run1/cns/begin/ before trying again.  

Hopt it will help u. Good luck.

WANG Xiao

Ph.D. Student

Paris Descartes University, Faculty of Pharmacy Therapeutic Targets and Drug Design -CiTCoM-UMR 8038

75270 Paris CEDEX 06 

   

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De : aria-discuss-request AT services.cnrs.fr <aria-discuss-request AT services.cnrs.fr> de la part de Julien CAPPELE <julien.cappele AT univ-lorraine.fr>
Envoyé : lundi 5 octobre 2020 14:08
À : aria-discuss AT services.cnrs.fr <aria-discuss AT services.cnrs.fr>
Objet : [aria-discuss] Structure calculation failing

 

Hello everyone,

I am sorry to disturb again, as I encountered another error, and again I can't understand what is wrong. I didn't find anything using google yet.

I have been able to compile CNS 1.2 and now it can be launched correctly from the terminal. On my project this time (not the tutorial of CcpNmr), I have set up an XML file for aria to work. Using the GUI, the project was completed and then I used :

$ aria2 -s test_aria.xml   # test_aria.xml is the name of the xml file that I used

$ aria2 test_aria.xml

Everything started and the structure calculation began. However, a few minutes later, I received some messages saying that the whole 20 structure calculation failed, and that I should check CNS output for errors. (I joined a screenshot in png format for you to see the output).

The thing is, the path to CNS output is empty. There are no cns files there. And I didn't find any files of use yet. Has anyone encountered a similar error?

There are multiple options that I can already consider :

1. I'm using google-drive ocamlfuse to work with my cloud, and maybe it is a problem for whatever reason. I can allocate more space to my ubuntu partition and do copy all the files to a local space. But i'm skeptical about that, it shouldn't be a problem.

2. CNS compiled without visible errors, but is not functional yet. I really don't know how to do better than I already did with my last question.

3. I could stop using local Aria and try AriaWeb but as I am new to NMR structure calculation, I do not know how to set up the parameters correctly. The jobs I tried to launch did not produce anything decent yet. My NMR supervisor also tried with one of her older projects that resulted with a publishable structure on Aria2 locally, but with AriaWeb she didn't get a good result either with the default parameters.

I have been struggling with these NMR structure calculations for over a month now, and starting to lose faith. Please help me, I don't really want to deal with bad x-ray diffraction nightmares again!

Thanks again,

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Julien Cappèle

Doctorant - 3ème année - ED C2MP

Université de Lorraine

CRM² - UMR CNRS 7036

julien.cappele@univ-lorraine.fr

Tel: (+33)6 99 18 59 03

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