Hey,
I am pretty certain that I have seen this problem before.
I think that in my case, it had to do with not compiling the relevant
CNS files that come with Aria.
Basically, the Aria installation has some extra CNS source files that
you need to compile with CNS.
Also, ccpnmr analysis has some python files that need to be moved into
the Aria directory. You should be able to file the relevent files
looking through the ARIA and analysis websites.
Does this help at all?
David
On 14-02-18 03:53 PM, Jaime Jensen wrote:
> Hello all,
>
> I am using CcpNmr Analysis 2.3.1, along with Aria 2.3.1 for structure calculations. I have completed the initial set-up in the Aria GUI, launched from Analysis. When running Aria, I get the following error:
>
> MESSAGE [Job manager]: shutdown.
> Traceback (most recent call last):
> File "/Users/usr//Software/aria2.3/aria2.py", line 903, in <module>
> verbose_level, use_condor=condor)
> File "/Users/usr//Software/aria2.3/aria2.py", line 813, in run_aria
> project.go(use_condor)
> File "/Users/usr/Software/aria2.3/src/py/aria/Project.py", line 1574, in go
> self.run_protocol(first_iteration)
> File "/Users/usr/Software/aria2.3/src/py/aria/Project.py", line 1580, in run_protocol
> last_iteration = self.getProtocol().go(iteration, self.getMolecule())
> File "/Users/usr/Software/aria2.3/src/py/aria/Protocol.py", line 1730, in go
> iteration = self.start(iteration, molecule)
> File "/Users/usr/Software/aria2.3/src/py/aria/Protocol.py", line 1714, in start
> return self.run_protocol(molecule, iteration)
> File "/Users/usr/Software/aria2.3/src/py/aria/Protocol.py", line 2182, in run_protocol
> is_first_it)
> File "/Users/usr/Software/aria2.3/src/py/aria/Protocol.py", line 2137, in run_iteration
> self.error(StandardError, err_msg)
> File "/Users/usr/Software/aria2.3/src/py/aria/ariabase.py", line 211, in error
> raise exception, msg
> StandardError: USER ERROR <aria.Protocol.Protocol> File "/Users/usr/Software/aria2.3/src/py/aria/Protocol.py", line 2182 in run_protocol
> Structure calculation failed for structure 1.
> Structure calculation failed for structure 2.
> Structure calculation failed for structure 3.
> Structure calculation failed for structure 4.
> Structure calculation failed for structure 5.
> Structure calculation failed for structure 6.
> Structure calculation failed for structure 7.
> Structure calculation failed for structure 8.
> Structure calculation failed for structure 9.
> Structure calculation failed for structure 10.
> Structure calculation failed for structure 11.
> Structure calculation failed for structure 12.
> Structure calculation failed for structure 13.
> Structure calculation failed for structure 14.
> Structure calculation failed for structure 15.
> Structure calculation failed for structure 16.
> Structure calculation failed for structure 17.
> Structure calculation failed for structure 18.
> Structure calculation failed for structure 19.
> Structure calculation failed for structure 20.
> Please check your setup and the CNS output files for errors.
>
> I am using default parameters, as this is my first Aria run for this structure.
>
> In the final refine.out file from CNS, I see the following error messages:
>
> %CNSsolve-ERR: unrecognized command:
> vean
> ^^^^
> %CNSsolve-ERR: unrecognized command:
> vean class
> ^^^^^
> %CNSsolve-ERR: unrecognized command:
> vean class vea1
> ^^^^
> %CNSsolve-ERR: unrecognized command:
> vean class vea1 force
> ^^^^^
> %CNSsolve-ERR: unrecognized command:
> vean class vea1 force $k_bor_1
> ^^^^^^^^
> %CNSsolve-ERR: unrecognized command:
> vean class vea1 force $k_bor_1 $k_cen_1
> ^^^^^^^^
> CNSsolve> vean class vea2 force $k_bor_2 $k_cen_2 end
> %CNSsolve-ERR: END LOOP expected:
> vean
> ^^^^
> %CNSsolve-ERR: unrecognized command:
> vean class
> ^^^^^
> %CNSsolve-ERR: unrecognized command:
> vean class vea2
> ^^^^
> %CNSsolve-ERR: unrecognized command:
> vean class vea2 force
> ^^^^^
> %CNSsolve-ERR: unrecognized command:
> vean class vea2 force $k_bor_2
> ^^^^^^^^
> %CNSsolve-ERR: unrecognized command:
> vean class vea2 force $k_bor_2 $k_cen_2
> ^^^^^^^^
> CNSsolve> vean class vea3 force $k_bor_3 $k_cen_3 end
> %CNSsolve-ERR: END LOOP expected:
> vean
> ^^^^
> %CNSsolve-ERR: unrecognized command:
> vean class
> ^^^^^
> %CNSsolve-ERR: unrecognized command:
> vean class vea3
> ^^^^
> %CNSsolve-ERR: unrecognized command:
> vean class vea3 force
> ^^^^^
> %CNSsolve-ERR: unrecognized command:
> vean class vea3 force $k_bor_3
> ^^^^^^^^
> %CNSsolve-ERR: unrecognized command:
> vean class vea3 force $k_bor_3 $k_cen_3
> ^^^^^^^^
> CNSsolve> vean class vea4 force $k_bor_4 $k_cen_4 end
> %CNSsolve-ERR: END LOOP expected:
> vean
> ^^^^
> %CNSsolve-ERR: unrecognized command:
> vean class
> ^^^^^
> %CNSsolve-ERR: unrecognized command:
> vean class vea4
> ^^^^
> %CNSsolve-ERR: unrecognized command:
> vean class vea4 force
> ^^^^^
> %CNSsolve-ERR: unrecognized command:
> vean class vea4 force $k_bor_4
> ^^^^^^^^
> %CNSsolve-ERR: unrecognized command:
> vean class vea4 force $k_bor_4 $k_cen_4
> ^^^^^^^^
> CNSsolve> vean class vea5 force $k_bor_5 $k_cen_5 end
> %CNSsolve-ERR: END LOOP expected:
> vean
> ^^^^
> %CNSsolve-ERR: unrecognized command:
> vean class
> ^^^^^
> %CNSsolve-ERR: unrecognized command:
> vean class vea5
> ^^^^
> %CNSsolve-ERR: unrecognized command:
> vean class vea5 force
> ^^^^^
> %CNSsolve-ERR: unrecognized command:
> vean class vea5 force $k_bor_5
> ^^^^^^^^
> %CNSsolve-ERR: unrecognized command:
> vean class vea5 force $k_bor_5 $k_cen_5
> ^^^^^^^^
> CNSsolve>
> CNSsolve> evaluate ($k_sani_1 = $k_sani_1 * $sani_fac_1)
> %CNSsolve-ERR: END LOOP expected:
> evaluate
> ^^^^^^^^
> %CNSsolve-ERR: unrecognized command:
> evaluate ($
> ^
> %CNSsolve-ERR: unrecognized command:
> evaluate ($k_sani_1
> ^^^^^^^^^
> %CNSsolve-ERR: unrecognized command:
> evaluate ($k_sani_1 =
> ^
> %CNSsolve-ERR: unrecognized command:
> evaluate ($k_sani_1 = $k_sani_1
> ^^^^^^^^^
> %CNSsolve-ERR: unrecognized command:
> evaluate ($k_sani_1 = $k_sani_1 *
> ^
> %CNSsolve-ERR: unrecognized command:
> evaluate ($k_sani_1 = $k_sani_1 * $sani_fac_1)
> ^^^^^^^^^^^
> %CNSsolve-ERR: unrecognized command:
> evaluate ($k_sani_1 = $k_sani_1 * $sani_fac_1)
> ^
> %PARSER error encountered: Encountered too many parsing errors.
> (CNS is in mode: SET ABORT=NORMal END)
> *****************************************************
> ABORT mode will terminate program execution.
> *****************************************************
> Program will stop immediately.
>
> Does anyone know what the problem may be, and perhaps a possible solution to this problem?
>
> Thank you!
>
|
