Discussion group for the ARIA software

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

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