Discussion group for the ARIA software

[Benjamin Bardiaux <bardiaux AT pasteur.fr>]

Dear Xiao,

You should have look at the CNS output files in runznc2/structures/it0/cns/.

One could also simply not import the Zn ion from CCPN (so just the 
protein chain). ARIA will (normally) add the Zn automatically.
Remove any previous psf and template in runznc2/cns/begin/ before trying 
again.

Best,

Benjamin

On 04/11/2019 10:10, Xiao Wang wrote:
> 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 PharmacieCibles Thérapeutiques et 
> Conception de Médicaments -CiTCoM-UMR 8038
>
> 75270 Paris CEDEX 06


--
---------------------------------------------
Dr Benjamin Bardiaux      bardiaux AT pasteur.fr
Unité de Bioinformatique Structurale
CNRS UMR3528 - Institut Pasteur
25,28 rue du Docteur Roux 75015 Paris, France
---------------------------------------------