Discussion group for the ARIA software

["Kelly, Mark" <Mark.Kelly AT ucsf.edu>]

Dear Benjamin,

we are having a similar problem to Xiao (below) - in it0, one to three structure calculations (cns) fail during the calculation (Aria2.3.1). We’ve tried changing the random seed and reversed the order of the Cys (Cys4). Is there anything else we can try?

Thanks, Mark

On Nov 13, 2019, at 7:42 AM, Xiao Wang <xiao.wang AT etu.parisdescartes.fr> wrote:

Hello, Benjamin,

As your suggestion, i changed the Random seed, it works.  Thanks for your help. 

WANG Xiao

Ph.D. Student

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

75270 Paris CEDEX 06 

   

---

De : Benjamin Bardiaux <bardiaux AT pasteur.fr>
Envoyé : vendredi 8 novembre 2019 21:16
À : Xiao Wang <xiao.wang AT etu.parisdescartes.fr>
Cc : aria-discuss AT services.cnrs.fr <aria-discuss AT services.cnrs.fr>; Serge Bouaziz <serge.bouaziz AT parisdescartes.fr>
Objet : Re: Structure calculation failed for structure 8.

 

Hi Xiao,

Maybe try to change the random seed number or inverse the order of the 2 cysteines in the Zn Patch panel (delete the psf and pdb files in cns/begin/ before restarting).

It’s also good to visualize the generated template in cns/begin/ to check if the Zn is correctly attached to the 1st cysteine listed in the Zn patch panel.

Best,

Benjamin 

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

Le 7 nov. 2019 à 17:15, Xiao Wang <xiao.wang AT etu.parisdescartes.fr> a écrit :



<Outlook-yxwrwxsy.png>

Many thanks, Benjamin,

Yes, i tried to only selected protein chain and set up a new run1,  it seems that the zinc error is solved.

But, i am sorry that a new error appears.  About  the protocol,  i made a test and set up the number of structures: 10 in the interaction 0.  
However, the aria can not calculate structure 8 and 9, only 8 and 9. 10 is good.  If i set every number of structures in the interactions is 7, it works well.

 The log is following:

  
MESSAGE [CNS]: CNS output files have been copied to /home/wangxiao/13C-15N-NEW-V
               PX2-ASSIGNMENT29052019/vpx30102019/vpx30102019/run1/structures/
               it0/cns
MESSAGE [Job manager]: shutdown.
Traceback (most recent call last):
  File "/home/wangxiao/PROGS/aria2.3//aria2.py", line 903, in <module>
    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 <aria.Protocol.Protocol> File "/home/wangxiao/PROGS/aria2.3/src/py/aria/Protocol.py" 
      , line 2300 in run_protocol

Please check your setup and the CNS output files for errors.



I check the refine_8.out   from  /home/wangxiao/13C-15N-NEW-VPX2-ASSIGNMENT29052019/vpx30102019/vpx30102019/run1/structures/it0/cns. The refine_8. out  is attached and  it is like:  

 -------------------------- Initial Conditions ---------------------------------
 | E(kin)+E(total)=63413.452       E(kin)=1984.307      temperature=4092.412   |
 | Etotal =61429.146  grad(E)=212.509    E(BOND)=41061.297  E(ANGL)=12392.880  |
 | E(IMPR)=4301.310   E(VDW )=974.838    E(CDIH)=1854.067   E(NOE )=844.754    |
 -------------------------------------------------------------------------------
 NBONDS: found    12192 intra-atom interactions
 NBONDS: found    12096 intra-atom interactions
 NBONDS: found    11973 intra-atom interactions
 NBONDS: found    11919 intra-atom interactions
 NBONDS: found    11914 intra-atom interactions
 NBONDS: found    11931 intra-atom interactions
 NBONDS: found    11938 intra-atom interactions
 NBONDS: found    11605 intra-atom interactions
 NBONDS: found    11602 intra-atom interactions
 NBONDS: found    11467 intra-atom interactions
 NBONDS: found    12259 intra-atom interactions
 NBONDS: found    12858 intra-atom interactions
 %ATMCHK-ERR: unknown coordinates for atom "   B-1   -MET -CB  "
 %ATMCHK-ERR: unknown coordinates for atom "   B-1   -MET -CG  "
 %ATMCHK-ERR: unknown coordinates for atom "   B-1   -MET -SD  "
 %ATMCHK-ERR: unknown coordinates for atom "   B-1   -MET -CE  "
 %ATMCHK-ERR: unknown coordinates for atom "   B-1   -MET -C   "
 %ATMCHK-ERR: unknown coordinates for atom "   B-1   -MET -O   "
 %ATMCHK-ERR: unknown coordinates for atom "   B-1   -MET -N   "
 %ATMCHK-ERR: unknown coordinates for atom "   B-1   -MET -CA  "
 %ATMCHK-ERR: unknown coordinates for atom "   B-2   -ALA -N   "
 %ATMCHK-ERR: unknown coordinates for atom "   B-2   -ALA -CA  "
 %ATMCHK-ERR: unknown coordinates for atom "   B-2   -ALA -CB  "


Could we have good solution for this?   

Thanks in advance.

Have a nice day.

---

De : aria-discuss-request AT services.cnrs.fr <aria-discuss-request AT services.cnrs.fr> de la part de Benjamin Bardiaux <bardiaux AT pasteur.fr>
Envoyé : mercredi 6 novembre 2019 22:30
À : aria-discuss AT services.cnrs.fr <aria-discuss AT services.cnrs.fr>
Objet : Re: [aria-discuss] zinc

 

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
---------------------------------------------

<refine_8.out>