Discussion group for the ARIA software

[Sebastien Alphonse <salphonse AT ccny.cuny.edu>]

Hello everyone,

I'm trying to solve the structure of a complex protein-ligand (NAD+) using ARIA2.1,

I modified CNS topology and parameter files to add NAD+ in them (using NAD+ CIF file from PHENIX and CNS script cns_import_cif​ to convert it in CNS format) , I have also modified some file in ARIA2.1 to add atoms name for NAD+ (atomnames.xml, iupac.xml, etc..)

It kind of worked out, meaning that ARIA was able to generate a template containing both protein and NAD, was also to go through the first steps (assignment, calibration etc.. ), but I have some sort of instability during the structure generation phase, where ARIA failed to generate a random number of structures (between 1 to 30 depending of the run, server used etc...) and stop with the following message : 

"StandardError: USER ERROR <aria.Protocol.Protocol> File "/home/sebastien/Programs/aria2.3NAD/src/py/aria/Protocol.py", line 2300 in run_protocol

Structure calculation failed for structure 23.

Structure calculation failed for structure 260.

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

CNS outputs (refine_xxx.out) of all the failed structures end with the the same error :

 

%ATMCHK-ERR: unknown coordinates for atom "   B-1   -NAD -H61A"

%ATMCHK error encountered: Unknown coordinates

   (CNS is in mode: SET ABORT=NORMal END)

 *****************************************************

 ABORT mode will terminate program execution.

 *****************************************************

 Program will stop immediately.

          ============================================================

           Maximum dynamic memory allocation:   121605448 bytes

           Maximum dynamic memory overhead:          4240 bytes

However if I just delete the temp directory, the CNS output of the failed structures and restart ARIA with a new velocity seed, ARIA is then able to generate the missing structure and continue to the next iteration.... where it will (or not, it looks to be completely random) fail again to calculate few structures (with the same "unknown coordinates for atoms ...." error ) , and I will have to repeat the same process over and over to go through the 8 iterations. 

Is there anything that I can do to fix these errors, ? 

Thank you 

Sebastien Alphonse

City College Center for Discovery and Innovation

CDI 2.314

85 Saint Nicholas Terrace

New York,  10031 NY