Discussion group for the ARIA software

[Julien CAPPELE <julien.cappele AT univ-lorraine.fr>]

Hi Benjamin,

Thanks for both your answer,

Regarding the run1 folder, the path /run/cns does exist, it is the /begin/ folder that doesn't. There are only 2 other folders called "protocols" and "toppar" in /run1/cns

I checked in the temporary folder that was generated, and I did find a file called refine.out, i'm sending it in attached files.

From what I'm seeing, the final error message is "%PARSER error encountered: Encountered too many parsing errors." at line 25 534.

Also, beginning at line 25 414, there are a bunch of unrecognized commands like "%CNSsolve-ERR: unrecognized command:"

Maybe those commands were not compiled correctly ? Would another fortran compiler than gfortran work better for CNS ?

Thanks again for your help,

---------------------------------------------

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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Le lun. 5 oct. 2020 à 12:02, Benjamin Bardiaux <bardiaux AT pasteur.fr> a écrit :

> However, I don't have a run1/cns/begin folder, which could indicate that CNS is still not fully functional on my computer...

According to your previous screenshot, it should be in /home/jcappele/google-drive/Doctorat/RMN/

> I still don't know what is wrong with it though...
>
> Have a nice day,
> ---------------------------------------------
> Julien Cappèle
> Doctorant - 2ème année - ED C2MP
> Université de Lorraine
> CRM² - UMR CNRS 7036
> julien.cappele@ <mailto:juliencappele AT gmail.com>univ-lorraine.fr
> <https://urldefense.com/v3/__http://univ-lorraine.fr__;!!JFdNOqOXpB6UZW0!4Heqt6us5iYyKK-SYUQf7ND6UFqKisi5xjiHyAfQGFN70H0wfOWKEqrjtTkp2Awbng$>*
> *
> Tel: (+33)6 99 18 59 03
> ---------------------------------------------
>
>
> Le lun. 5 oct. 2020 à 10:30, Xiao Wang <xiao.wang AT etu.parisdescartes.fr <mailto:xiao.wang AT etu.parisdescartes.fr>> a écrit :
>
>     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
>
>
>     ------------------------------------------------------------------------------------------------------------------------
>     *De :* aria-discuss-request AT services.cnrs.fr <mailto:aria-discuss-request AT services.cnrs.fr>
>     <aria-discuss-request AT services.cnrs.fr <mailto:aria-discuss-request AT services.cnrs.fr>> de la part de Julien CAPPELE
>     <julien.cappele AT univ-lorraine.fr <mailto:julien.cappele AT univ-lorraine.fr>>
>     *Envoyé :* lundi 5 octobre 2020 14:08
>     *À :* aria-discuss AT services.cnrs.fr <mailto:aria-discuss AT services.cnrs.fr> <aria-discuss AT services.cnrs.fr
>     <mailto: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,
>     ---------------------------------------------
>     Julien Cappèle
>     Doctorant - 3ème année - ED C2MP
>     Université de Lorraine
>     CRM² - UMR CNRS 7036
>     julien.cappele@ <mailto:juliencappele AT gmail.com>univ-lorraine.fr
>     <https://urldefense.com/v3/__http://univ-lorraine.fr__;!!JFdNOqOXpB6UZW0!4Heqt6us5iYyKK-SYUQf7ND6UFqKisi5xjiHyAfQGFN70H0wfOWKEqrjtTkp2Awbng$>*
>     *
>     Tel: (+33)6 99 18 59 03
>     ---------------------------------------------
>


--
---------------------------------------------
Dr Benjamin Bardiaux      bardiaux AT pasteur.fr
Unité de Bioinformatique Structurale
CNRS UMR3528 - Institut Pasteur
25,28 rue du Docteur Roux 75015 Paris, France
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Attachment: refine.out
Description: Binary data