Discussion group for the ARIA software

[Xiao Wang <xiao.wang AT etu.parisdescartes.fr>]

Hello everyone,

I used analysis project and calculate structure , it works good.

But, I added zinc into analysis 2.4.2 and aria 2.3.2. In aria, the type of coordination is Cys2HisdHise(CCHdHe). my binding amino H46, H89, C94, and C96. HIS patches are 46  89 HISD HISE.

 it did not work. The log is following:

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 "vpx31102019ZNC.xml"...
MESSAGE [Project]: Temporary directory has been set to /home/wangxiao/
                   13C-15N-NEW-VPX2-ASSIGNMENT29052019/vpx30102019/VPX30102019_1
                   /aria_temp.tmpf2TZUz1572537230
MESSAGE [Project]: List of available machines is empty. Running calculations on
                   localhost "laurier", assuming 1 CPU. Using /home/wangxiao/
                   PROGS/cns_solve_1.21/intel-x86_64bit-linux/bin/cns as
                   structure engine.
MESSAGE [Project]: Checking host list ...
MESSAGE [Job manager]: Command "csh -f" ... ok.
MESSAGE [Project]: Cache is disabled.
Model read finished. Duration 0.894804000854
Model validity check skipped
MESSAGE [Project]: ------------ Reading data from CCPN data model ------------
MESSAGE [Project]: Opening CCPN data model "/home/wangxiao/13C-15N-NEW-VPX2-ASSI
                   GNMENT29052019/vpx30102019/VPX30102019_1/vpx30102019"...
MESSAGE [Project]: CCPN data model opened.
MESSAGE [Project]: Retrieving molecular system "MS1", chain code(s) "B,C"...
MESSAGE [Project]: Retrieving Constraint List "2|1" of type "dihedrals" ...
MESSAGE [Project]: Retrieving peak list "(project=vpx30102019, experiment=2,
                   data_source=1, serial=1)", shift list "1" ...
WARNING [Chain]: Residue ZN not known.
MESSAGE [Project]: CCPN Contraints list 2|1 written to /home/wangxiao/
                   13C-15N-NEW-VPX2-ASSIGNMENT29052019/vpx30102019/VPX30102019_1
                   /runznc2/data/dihedrals/2_1.tbl.
MESSAGE [Project]: CCPN import done.
MESSAGE [Project]: ------------------- Filtering input data -------------------
MESSAGE [Project]: Applying filters to spectrum/shiftlist "NOESY114":
MESSAGE [Project]: Chemical shift list filtered: 0 / 853 shifts (0.00 %)
                   removed.
MESSAGE [Project]: NOESY spectrum "NOESY114" filtered: 250 / 1103 peaks (22.67
                   %) 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:          205
MESSAGE [Project]: - no. of unassigned peaks:        45
WARNING [NOESYSpectrumFilter.TP]: Path "/home/wangxiao/13C-15N-NEW-VPX2-ASSIGNME
                                  NT29052019/vpx30102019/VPX30102019_1/runznc2/
                                  data/spectra/peak_list.filtered" already
                                  exists and will be overwritten.
MESSAGE [NOESYSpectrumFilter.TP]: Spectrum filter report written to file "/home/
                                  wangxiao/13C-15N-NEW-VPX2-ASSIGNMENT29052019/
                                  vpx30102019/VPX30102019_1/runznc2/data/
                                  spectra/peak_list.filtered"
MESSAGE [Project]: ---------------- Preparing structure engine ----------------
WARNING [CNS]: Existing copy "/home/wangxiao/13C-15N-NEW-VPX2-ASSIGNMENT29052019
               /vpx30102019/VPX30102019_1/runznc2/cns/data/dihedrals/dihedrals_t
               alos.tbl" has been removed and will be replaced by a new copy.
WARNING [CNS]: File "/home/wangxiao/13C-15N-NEW-VPX2-ASSIGNMENT29052019/
               vpx30102019/VPX30102019_1/runznc2/cns/data/sequence/vpx30102019_Z
               N.pdb" does already exist and will be overwritten.
MESSAGE [CNS]: Sequence PDB-file written.
MESSAGE [CNS]: PSF-file already exists. Using existing file: vpx30102019_ZN.psf
MESSAGE [CNS]: Template PDB file (/home/wangxiao/13C-15N-NEW-VPX2-ASSIGNMENT2905
               2019/vpx30102019/VPX30102019_1/runznc2/cns/begin/vpx30102019_ZN_t
               emplate.pdb) does already exist. Using existing file.
MESSAGE [Project]: Starting ARIA main protocol on Thu Oct 31 16:54:02 2019
MESSAGE [Project]: -------------------- Assigning spectra --------------------
MESSAGE [Project]: Creating seed assignment for spectrum "NOESY114" ...
MESSAGE [Project]: Done. 0 / 853 peaks (0.00 %) could not be assigned (s. peak
                   assigner report file for details).
WARNING [Assigner.TP]: PeakAssigner report file /home/wangxiao/13C-15N-NEW-VPX2-
                       ASSIGNMENT29052019/vpx30102019/VPX30102019_1/runznc2/
                       data/spectra/peak_list.unassigned already exists and
                       will be overwritten.
MESSAGE [Protocol]: ---------------------- Iteration 0 -----------------------

MESSAGE [Protocol]: Calibrating spectrum "NOESY114"...
MESSAGE [Protocol]: Peaks merged: 389 / 853 peaks (45.6 %) (see report for
                    details).
WARNING [CNS]: File /home/wangxiao/13C-15N-NEW-VPX2-ASSIGNMENT29052019/
               vpx30102019/VPX30102019_1/runznc2/structures/it0/unambig.tbl
               does already exist and will be overwritten
WARNING [CNS]: File /home/wangxiao/13C-15N-NEW-VPX2-ASSIGNMENT29052019/
               vpx30102019/VPX30102019_1/runznc2/structures/it0/ambig.tbl does
               already exist and will be overwritten
MESSAGE [Job]: Starting job: "cd /home/wangxiao/13C-15N-NEW-VPX2-ASSIGNMENT29052
               019/vpx30102019/VPX30102019_1/aria_temp.tmpf2TZUz1572537230/
               run_cns_2; csh -f /home/wangxiao/13C-15N-NEW-VPX2-ASSIGNMENT29052
               019/vpx30102019/VPX30102019_1/aria_temp.tmpf2TZUz1572537230/
               run_cns_2/refine.csh &"
MESSAGE [Protocol]: Waiting for completion of structure calculation...
MESSAGE [Job]: Job "cd /home/wangxiao/13C-15N-NEW-VPX2-ASSIGNMENT29052019/
               vpx30102019/VPX30102019_1/aria_temp.tmpf2TZUz1572537230/
               run_cns_2; csh -f /home/wangxiao/13C-15N-NEW-VPX2-ASSIGNMENT29052
               019/vpx30102019/VPX30102019_1/aria_temp.tmpf2TZUz1572537230/
               run_cns_2/refine.csh &" completed.
MESSAGE [Job]: Starting job: "cd /home/wangxiao/13C-15N-NEW-VPX2-ASSIGNMENT29052
               019/vpx30102019/VPX30102019_1/aria_temp.tmpf2TZUz1572537230/
               run_cns_1; csh -f /home/wangxiao/13C-15N-NEW-VPX2-ASSIGNMENT29052
               019/vpx30102019/VPX30102019_1/aria_temp.tmpf2TZUz1572537230/
               run_cns_1/refine.csh &"
MESSAGE [Job]: Job "cd /home/wangxiao/13C-15N-NEW-VPX2-ASSIGNMENT29052019/
               vpx30102019/VPX30102019_1/aria_temp.tmpf2TZUz1572537230/
               run_cns_1; csh -f /home/wangxiao/13C-15N-NEW-VPX2-ASSIGNMENT29052
               019/vpx30102019/VPX30102019_1/aria_temp.tmpf2TZUz1572537230/
               run_cns_1/refine.csh &" completed.
MESSAGE [CNS]: CNS output files have been copied to /home/wangxiao/13C-15N-NEW-V
               PX2-ASSIGNMENT29052019/vpx30102019/VPX30102019_1/runznc2/
               structures/it0/cns
MESSAGE [Job manager]: shutdown.
Traceback (most recent call last):
  File "/home/wangxiao/PROGS/aria2.3//aria2.py", line 903, in
    verbose_level, use_condor=condor)
  File "/home/wangxiao/PROGS/aria2.3//aria2.py", line 813, in run_aria
    project.go(use_condor)
  File "/home/wangxiao/PROGS/aria2.3/src/py/aria/Project.py", line 1666, in go
    self.run_protocol(first_iteration)
  File "/home/wangxiao/PROGS/aria2.3/src/py/aria/Project.py", line 1672, in run_protocol
    last_iteration = self.getProtocol().go(iteration, self.getMolecule())
  File "/home/wangxiao/PROGS/aria2.3/src/py/aria/Protocol.py", line 1841, in go
    iteration = self.start(iteration, molecule)
  File "/home/wangxiao/PROGS/aria2.3/src/py/aria/Protocol.py", line 1825, in start
    return self.run_protocol(molecule, iteration)
  File "/home/wangxiao/PROGS/aria2.3/src/py/aria/Protocol.py", line 2300, in run_protocol
    is_first_it)
  File "/home/wangxiao/PROGS/aria2.3/src/py/aria/Protocol.py", line 2255, in run_iteration
    self.error(StandardError, err_msg)
  File "/home/wangxiao/PROGS/aria2.3/src/py/aria/ariabase.py", line 211, in error
    raise exception, msg
StandardError: USER ERROR File "/home/wangxiao/PROGS/aria2.3/src/py/aria/Protocol.py", line 2300 in run_protocol
Structure calculation failed for structure 1.
Structure calculation failed for structure 2.
Please check your setup and the CNS output files for errors.


any good suggestion?

WANG Xiao

Ph.D. Student

Université Paris Descartes, Faculté de Pharmacie Cibles Thérapeutiques et Conception de Médicaments -CiTCoM-UMR 8038

75270 Paris CEDEX 06