Discussion group for the ARIA software

[Benjamin Bardiaux <bardiaux AT pasteur.fr>]

Dear Clara,

This should be doable in principle. Could send me your ccpn and aria projects in private ? I will try to see what goes wrong.

Best,

Benjamin 

-----------------------------------------------------
Dr Benjamin Bardiaux    | Bioinformatique Structurale
bardiaux AT pasteur.fr     | Institut Pasteur
25,28 rue du Docteur Roux 75015 Paris, France
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Le 2 déc. 2022 à 16:38, Clara Morguet <clara.morguet AT tum.de> a écrit :

Hello,

I am trying to perform structure calculation of a complex composed of RNA and
a Zn-finger protein with Aria 2.3.2 but have problems defining the molecular
system.
When using the molecule sequences from a ccpNmr project (version 2.4.2), Aria
cannot recognize the RNA sequence.
When creating an XML file for defining the molecular system, Aria is able to
perform structure calculation of the protein-RNA complex, but only without the
Zinc. As soon as the Zinc coordination is implemented, no matter whether the
ion is listed in the XML file or not, the protein sequence is disrupted.
Instead of a polymer chain in the template pdb file, there are only single
amino acids and structure calculations fail. The RNA sequence stays intact. I
evaluated that the implementation of Zinc coordination and HIS patch is
correct as it is possible to calculate structures with defining the molecular
system through ccpNmr (without the RNA).

Is there a way to define the Zinc in the XML file without disrupting the
protein sequence? Or is it possible to define the RNA in ccpNmr in a way that
can be read by Aria?

Thank you in advance for your help!
Best wishes
Clara

Error in output file when defining the molecular system including RNA via
ccpNmr
MESSAGE [Project]: CCPN data model opened.
MESSAGE [Project]: Retrieving molecular system "Prot_RNA", chain code(s)
                  "A,B,C,D,E"...
WARNING [Chain]: Residue U not known.
WARNING [Chain]: Residue A not known.
WARNING [Chain]: Residue U not known.
WARNING [Chain]: Residue A not known.
WARNING [Chain]: Residue C not known.
WARNING [Chain]: Residue U not known.
WARNING [Chain]: Residue A not known.
WARNING [Chain]: Residue C not known.
MESSAGE [Project]: CCPN import done.


Error in cns output files when defining the molecular system by an XML file:

DTOREST2: number of groups       1358
DTOREST2: number of joints       1123
DTOREST2: total number of closed loops          0
DTOREST2: number of trees        235
DTOREST2: total number of chains        755
DTOREST2: maximum number of chains in any tree         29
DTOREST2: overall maximum chain length          5
-------------------------- Torsion Topology
-----------------------------------
Please send a bug report to brunger AT stanford.edu
         Please increase MAXTREE and re-run.

%TORSION:TOPOLOGY error encountered: Fatal Topology Error
  (CNS is in mode: SET ABORT=NORMal END)
*****************************************************
ABORT mode will terminate program execution.
*****************************************************
Program will stop immediately.