Discussion group for the ARIA software

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

Hi everyone,

I am new to the ARIA software. I was able to install it properly and test it
using the tutorial files available on the ARIA website and it ran smoothly.
For my  data, I was able to convert my NMRView files (.xpk and chemicial
shifts)  into ARIA format based on the instructions provided in the tutorials
(i.e. conversion.xml). I followed the instructions and also set up the proper
parameters on the GUI to the best of my knowledge. However, during the actual
structure calculation i.e. running my project file it tends to show an error
stating that "More than 90% of the cross peaks could not be assigned. This
might be due to interchanged frequency dimensions or undersized frequency
windows. Please check your setup." I am testing it on a 13C NOESY spectrum so
I set the proton2 dimension to 0.02 and the proton1 dimension to 0.04. The
same error appears whenever I try using my 15N NOESY spectrum.

I was able to run before, but suddenly it just stopped working and kept on
showing this error.  There must be something wrong at my end, which I cannot
seem to figure out. Any advice would be highly appreciated to remedy the
matter.

I pasted the error below:
######################################################################################
pmh-j:rafid% aria2 test_project.xml

ARIA Version 2.3.2. Authors: Benjamin Bardiaux, Michael Habeck, Jens Linge,
Therese Malliavin, Sean O'Donoghue, Wolfgang Rieping, and Michael Nilges.

If you use this software, please quote the following reference(s):

Rieping W., Habeck M., Bardiaux B., Bernard A., Malliavin T.E.,
Nilges M.(2007) ARIA2: automated NOE assignment and data integration in NMR
structure calculation. Bioinformatics 23:381-382


Loading project "test_project.xml"...
MESSAGE [Project]: Temporary directory has been set to /home/rafid/NMR/
ArlR_DBD/
                   NOE02/AriaTest_Sep27_2021/aria_temp.tmp6rqxhC1632792952
MESSAGE [Project]: List of available machines is empty. Running calculations
on
                   localhost "pmh-j", assuming 1 CPU. Using /usr/local/
                   cns_solve_1.21/intel-x86_64bit-linux/bin/cns_solve as
                   structure engine.
MESSAGE [Project]: Checking host list ...
MESSAGE [Job manager]: Command "csh -f" ... ok.
MESSAGE [Project]: -------------------- Reading data --------------------
MESSAGE [Project]: Cache is enabled.
MESSAGE [Project]: Loading cached data files...
MESSAGE [Project]: Reading molecule definition /home/rafid/NMR/ArlR_DBD/NOE02/
                   AriaTest_Sep27_2021/run1/data/sequence/test_seq.xml.
MESSAGE [Project]: Reading spectrum /home/rafid/NMR/ArlR_DBD/NOE02/
AriaTest_Sep2
                   7_2021/run1/data/spectra/13C_peaks.xml.
MESSAGE [Project]: Reading chemical shift list /home/rafid/NMR/ArlR_DBD/NOE02/
                   AriaTest_Sep27_2021/run1/data/spectra/13Ctestppm.xml.
MESSAGE [Project]: Data files read.
MESSAGE [Project]: ------------------- Filtering input data
-------------------
MESSAGE [Project]: Applying filters to spectrum/shiftlist "13CNOESY":
MESSAGE [Project]: Chemical shift list filtered: 421 / 1288 shifts (32.69 %)
                   removed.
MESSAGE [Project]: NOESY spectrum "13CNOESY" filtered: 0 / 1173 peaks (0.00 %)
                   removed. Details:
MESSAGE [Project]: - no. of invalid proton 1 shifts: 0
MESSAGE [Project]: - no. of invalid proton 2 shifts: 0
MESSAGE [Project]: - no. of invalid peak sizes:      0
MESSAGE [Project]: - no. of diagonal peaks:          0
MESSAGE [Project]: - no. of unassigned peaks:        0
WARNING [NOESYSpectrumFilter.TP]: Path "/home/rafid/NMR/ArlR_DBD/NOE02/
                                  AriaTest_Sep27_2021/run1/data/spectra/
                                  peak_list.filtered" already exists and will
                                  be overwritten.
MESSAGE [NOESYSpectrumFilter.TP]: Spectrum filter report written to file "/
home/
                                  rafid/NMR/ArlR_DBD/NOE02/
AriaTest_Sep27_2021/
                                  run1/data/spectra/peak_list.filtered"
MESSAGE [Project]: ---------------- Preparing structure engine
----------------
WARNING [CNS]: Existing copy "/home/rafid/NMR/ArlR_DBD/NOE02/
AriaTest_Sep27_2021
               /run1/cns/data/dihedrals/dihedrals.tbl" has been removed and
               will be replaced by a new copy.
WARNING [CNS]: File "/home/rafid/NMR/ArlR_DBD/NOE02/AriaTest_Sep27_2021/run1/
               cns/data/sequence/test_struct.pdb" does already exist and will
               be overwritten.
MESSAGE [CNS]: Sequence PDB-file written.
MESSAGE [CNS]: PSF-file already exists. Using existing file: test_struct.psf
MESSAGE [CNS]: Template PDB file (/home/rafid/NMR/ArlR_DBD/NOE02/
AriaTest_Sep27_
               2021/run1/cns/begin/test_struct_template.pdb) does already
               exist. Using existing file.
MESSAGE [Project]: Starting ARIA main protocol on Mon Sep 27 19:35:52 2021
MESSAGE [Project]: -------------------- Assigning spectra --------------------
MESSAGE [Project]: Creating seed assignment for spectrum "13CNOESY" ...
WARNING [Project]: More than 90% of the cross peaks could not be assigned.
This
                   might be due to interchanged frequency dimensions or
                   undersized frequency windows. Please check your setup.

ARIA halted at Mon Sep 27 19:35:53 2021.
######################################################################################################
Please let me know if you require any further information from my end.

Thanks.
Regards,

Rafid