Discussion group for the ARIA software

[Benjamin Bardiaux <bardiaux AT pasteur.fr>]

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