Discussion group for the ARIA software

[Mohammad Rafid Feisal <rafidfei AT ualberta.ca>]

Dear Benjamin, 

That has definitely resolved the issue. I thought that might be the problem, but figured it's too trivial. Thank you for solving my problem. It's running now. 

Thanks again. 

Regards, 

Rafid Feisal

On Tue, Oct 17, 2023 at 12:58 AM Benjamin Bardiaux <aria-discuss AT services.cnrs.fr> wrote:

Dear Rafid,

CNS is quite an old software that has a length limit on directory paths.

In you case, your path
/home/rafid/NMR/ArlR_DBD/NOE02/
StructureCalculations_Final/Aria_Web_2023/AriaWeb_Run12_Oct6_2023/
is too long for CNS.

Please try and shorten the absolute path, possibly with less explicit folder names.

Best,

Benjamin
---------------------------------------------
Dr Benjamin Bardiaux      bardiaux AT pasteur.fr
Bacterial Transmembrane Systems Unit (BaTS)
CNRS UMR 3528 - Institut Pasteur
25,28 rue du Docteur Roux 75015 Paris, France
---------------------------------------------

> Le 17 oct. 2023 à 04:05, Rafid Feisal <aria-discuss AT services.cnrs.fr> a écrit :
>
> Hi everyone,
>
> I am currently trying to run structure calculations on a local installation.
> Haven't used my local installation in a while since I have been using ARIA
> Web. I tried running and this is part of the error that pops up in my
> terminal:
>
> MESSAGE [CNS]: Sequence PDB-file written.
> MESSAGE [CNS]: CNS output file has been copied to "/home/rafid/NMR/ArlR_DBD/
>               NOE02/StructureCalculations_Final/Aria_Web_2023/
> AriaWeb_Run12_Oct
>               6_2023/run1/cns/begin/generate.out".
> Traceback (most recent call last):
>  File "/usr/local/aria2.3/aria2.py", line 903, in <module>
>    verbose_level, use_condor=condor)
>  File "/usr/local/aria2.3/aria2.py", line 813, in run_aria
>    project.go(use_condor)
>  File "/usr/local/aria2.3/src/py/aria/Project.py", line 1665, in go
>    first_iteration = self.finalize()
>  File "/usr/local/aria2.3/src/py/aria/Project.py", line 1650, in finalize
>    protocol.finalize_engine(self.getMolecule())
>  File "/usr/local/aria2.3/src/py/aria/Protocol.py", line 1626, in
> finalize_engine
>    engine.prepare(self.getSettings(), molecule)
>  File "/usr/local/aria2.3/src/py/aria/cns.py", line 2038, in prepare
>    self.create_psf_file(protocol_settings, replace)
>  File "/usr/local/aria2.3/src/py/aria/cns.py", line 1925, in create_psf_file
>    self.error(IOError, s % psf_file)
>  File "/usr/local/aria2.3/src/py/aria/ariabase.py", line 211, in error
>    raise exception, msg
> IOError: USER ERROR <aria.cns.CNS> File "/usr/local/aria2.3/src/py/aria/
> cns.py", line 2038 in prepare
> An error occurered during creation of the PSF-file: "/home/rafid/NMR/ArlR_DBD/
> NOE02/StructureCalculations_Final/Aria_Web_2023/AriaWeb_Run12_Oct6_2023/run1/
> cns/begin/ArlRDBD_Run12_Oct6_2023.psf" could not be found.
>
> I believe it is not an issue with Aria but rather with CNS.
> This is the output in the generate.out file (/run1/cns/begin/generate.out):
>
>          ============================================================
>          |                                                          |
>          |            Crystallography & NMR System (CNS)            |
>          |                         CNSsolve                         |
>          |                                                          |
>          ============================================================
>           Version: 1.2 at patch level 1
>           Status: General release with ARIA enhancements
>          ============================================================
>           Written by: A.T.Brunger, P.D.Adams, G.M.Clore, W.L.DeLano,
>                       P.Gros, R.W.Grosse-Kunstleve, J.-S.Jiang,
>                       J.Kuszewski, M.Nilges, N.S.Pannu, R.J.Read,
>                       L.M.Rice, T.Simonson, G.L.Warren.
>           Copyright (c) 1997-2007 Yale University
>          ============================================================
>           Running on machine: pmh-j (x86_64/Linux,64-bit)
>           Program started by: rafid
>           Program started at: 19:54:07 on 16-Oct-2023
>          ============================================================
>
> FFT3C: Using FFTPACK4.1
>
> CNSsolve>!$Revision: 1.1.1.1 $
> CNSsolve>!$Date: 2010/03/23 15:27:16 $
> CNSsolve>!$RCSfile: generate.inp,v $
> CNSsolve>
> CNSsolve>!     ************************************
> CNSsolve>!     * Authors and copyright:           *
> CNSsolve>!     * Michael Nilges, Jens Linge, EMBL *
> CNSsolve>!     * No warranty implied or expressed *
> CNSsolve>!     * All rights reserved              *
> CNSsolve>!     ************************************
> CNSsolve>
> CNSsolve>@RUN_CNS:run.cns(
> ASSFIL: file run.cns opened.
> CNSsolve>!$Revision: 1.1.1.1 $
> CNSsolve>!$Date: 2010/03/23 15:27:26 $
> CNSsolve>!$RCSfile: run.cns,v $
> CNSsolve>
> CNSsolve>module(
> MODULE-DECLARATION>spectrum;
> MODULE-DECLARATION>filenames;
> MODULE-DECLARATION>spectra;
> MODULE-DECLARATION>data;
> MODULE-DECLARATION>iterations;
> MODULE-DECLARATION>saprotocol;
> MODULE-DECLARATION>refine;
> MODULE-DECLARATION>relax;
> MODULE-DECLARATION>toppar;
> MODULE-DECLARATION>analysis;
> MODULE-DECLARATION>)
> MODULE-INVOCATION>spectrum  =$spectrum;
> &_2_SPECTRUM set to $_1_SPECTRUM
> MODULE-INVOCATION>filenames =$filenames;
> &_2_FILENAMES set to $_1_FILENAMES
> MODULE-INVOCATION>spectra   =$spectra;
> &_2_SPECTRA set to $_1_SPECTRA
> MODULE-INVOCATION>data      =$data;
> &_2_DATA set to $_1_DATA
> MODULE-INVOCATION>iterations=$iterations;
> &_2_ITERATIONS set to $_1_ITERATIONS
> MODULE-INVOCATION>saprotocol=$saprotocol;
> &_2_SAPROTOCOL set to $_1_SAPROTOCOL
> MODULE-INVOCATION>refine    =$refine;
> &_2_REFINE set to $_1_REFINE
> MODULE-INVOCATION>relax     =$relax;
> &_2_RELAX set to $_1_RELAX
> MODULE-INVOCATION>toppar    =$toppar;
> &_2_TOPPAR set to $_1_TOPPAR
> MODULE-INVOCATION>analysis  =$analysis;
> &_2_ANALYSIS set to $_1_ANALYSIS
> MODULE-INVOCATION>)
> CNSsolve>
> CNSsolve>{+ file: run.cns +}
> CNSsolve>{+ description: The file run.cns contains all necessary information
> to run ARIA. ARIA automatically sets the default values.
> CNSsolve>Please change the values for the mixing time, rotation
> CNSsolve>correlation time and spectrometer frequency for the spin diffusion
> correction.
> CNSsolve>For the large CNS log files, you should use a temporary directory.
> version 1.2 +}
> CNSsolve>{+ authors: Jens Linge, Michael Nilges +}
> CNSsolve>
> CNSsolve>set message off echo off end
> CNSsolve>
> CNSsolve>
> CNSsolve>
> CNSsolve>
> CNSsolve>!============= aria2.0 ==============
> CNSsolve>
> CNSsolve>!evaluate ($iteration = $data.iteration)
> CNSsolve>
> CNSsolve>evaluate($prot_top_file_1= "RUN:toppar/" + $Toppar.prot_top_1)
> EVALUATE: symbol $PROT_TOP_FILE_1 set to
> "RUN:toppar/topallhdg5.3.pro" (string)
> CNSsolve>evaluate($prot_top_file_2= "")
> EVALUATE: symbol $PROT_TOP_FILE_2 set to "" (string)
> CNSsolve>if ($Toppar.prot_top_2 ne "") then
> NEXTCD: condition evaluated as false
> CNSsolve>  evaluate($prot_top_file_2= "RUN:toppar/" + $Toppar.prot_top_2)
> CNSsolve>end if
> CNSsolve>evaluate($prot_link_file_1= "RUN:toppar/" + $Toppar.prot_link_1)
> EVALUATE: symbol $PROT_LINK_FILE_1 set to
> "RUN:toppar/topallhdg5.3.pep" (string)
> CNSsolve>evaluate($prot_link_file_2= "")
> EVALUATE: symbol $PROT_LINK_FILE_2 set to "" (string)
> CNSsolve>if ($Toppar.prot_link_2 ne "") then
> NEXTCD: condition evaluated as false
> CNSsolve>  evaluate($prot_link_file_2= "RUN:toppar/" + $Toppar.prot_link_2)
> CNSsolve>end if
> CNSsolve>evaluate($sequence_file= "RUN:data/sequence/" + $Toppar.prot_coor_1)
> EVALUATE: symbol $SEQUENCE_FILE set to
> "RUN:data/sequence/ArlRDBD_Run12_Oct6_2023.pdb" (string)
> CNSsolve>
> CNSsolve>topology
> RTFRDR>   @@$prot_top_file_1
> ASSFIL: file topallhdg5.3.pro opened.
> RTFRDR>remark   file topallhdg.pro  version 5.3  date 13-Feb-02
> RTFRDR>remark      for file parallhdg.pro version 5.3 date 13-Feb-02 or later
> RTFRDR>remark   Geometric energy function parameters for distance geometry
> and
> RTFRDR>remark      simulated annealing.
> RTFRDR>remark   Author: Michael Nilges, EMBL Heidelberg; Institut Pasteur,
> Paris
> RTFRDR>remark   This file contains modifications from M. Williams, UCL London
> RTFRDR>remark   Last modification 13-Feb-02
> RTFRDR>
> RTFRDR>set echo off message off end
> RTFRDR>   if ($prot_top_file_2 ne "") then
> RTFRDR>    @@$prot_top_file_2
> RTFRDR>   end if
> RTFRDR>end
> CNSsolve>
> CNSsolve>!for the case, that you don't want a SEGID:
> CNSsolve>if ($Toppar.prot_segid_1="") then
> CNSsolve>   evaluate($Toppar.prot_segid_1="    ")
> CNSsolve>end if
> CNSsolve>
> CNSsolve>segment
> SEGMENT>   name=$Toppar.prot_segid_1
> SEGMENT>   chain
> CHAIN>      separate-by-segid=true
> CHAIN>      @$prot_link_file_1
> CHAIN>REMARKS  TOPH19.pep -MACRO for protein sequence
> CHAIN>SET ECHO=FALSE END
> CHAIN>      if ($prot_link_file_2 ne "") then
> CHAIN>         @$prot_link_file_2
> CHAIN>      end if
> CHAIN>      if ($Toppar.pdb_or_sequence="sequence") then
> CHAIN>         sequence @@$sequence_file END         !for sequence file
> CHAIN>      else
> CHAIN>         coor @@$sequence_file                 !for PDB file
> SEGMNT: sequence read from coordinate file
> %ADDST-ERR: STMAX too small. Check code
> %ASSFIL-ERR: error opening file /home/rafid/NMR/ArlR_DBD/NOE02/
> StructureCalculations_Final/Aria_Web_2023/AriaWeb_Run12_Oct6_2023/run1/cns/
> %ASSFIL error encountered: Error accessing file
>   (CNS is in mode: SET ABORT=NORMal END)
> *****************************************************
> ABORT mode will terminate program execution.
> *****************************************************
> Program will stop immediately.
>          ============================================================
>           Maximum dynamic memory allocation:     8201488 bytes
>           Maximum dynamic memory overhead:           208 bytes
>           Program started at: 19:54:07 on 16-Oct-2023
>           Program stopped at: 19:54:07 on 16-Oct-2023
>           CPU time used:       0.0093 seconds
>          ============================================================
>
> It seems to be an issue with gfortran the compiler based on a similar post
> from earlier. It must have gotten updated at some point. However, I am pretty
> confused as to how to remedy the matter.
>
> Any advice would be highly appreciated.
>
> Thanks.
> Rafid Feisal