Discussion group for the ARIA software

["Higman, Vicky (Dr.)" <vad5 AT leicester.ac.uk>]

Hi Mark,

try using the parameters suggested in table S5 in the supplementary info of the Mareuil et al. 2015 paper. I have generally had good experiences with that. Note in particular the number of SA high temp and cooling steps - these are much larger than what is typically used.

All the best,

Vicky

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From: aria-discuss-request AT services.cnrs.fr <aria-discuss-request AT services.cnrs.fr> on behalf of Kelly, Mark <Mark.Kelly AT ucsf.edu>
Sent: 02 June 2020 18:17
To: aria-discuss AT services.cnrs.fr <aria-discuss AT services.cnrs.fr>
Cc: Benjamin Bardiaux <bardiaux AT pasteur.fr>; Longbotham, James <James.Longbotham AT ucsf.edu>
Subject: Re: [aria-discuss] Next step in calculations

 

Hello All,

we switched ‘on’ the log harmonic potential, but now our structures don’t look very nice. I wonder if we did not set the parameters correctly or do we have to switch something else off?

Best,

Mark

<logharmonic_potential enabled="yes" use_auto_weight="yes" weight_unambig="1.0" weight_ambig="1.0" weight_hbond="1.0"/>

On Apr 29, 2020, at 10:50 AM, Kelly, Mark <Mark.Kelly AT ucsf.edu> wrote:

Hello All,

we tried to restart a run that had been successful before and get the error below - would anyone have a suggestion what might be wrong?

hope all are safe and well,

Mark

Begin forwarded message:

From: "Longbotham, James" <James.Longbotham AT ucsf.edu>

Subject: RE: Next step in calculations

Date: April 29, 2020 at 10:37:57 AM PDT

To: "Kelly, Mark" <Mark.Kelly AT ucsf.edu>

Ok so that last run I  described below failed. I thought it ould have something to do with the merged restraint lists so I tried to run it again with the restraints I used previously (before assignment) and it failed still! See error below. Not sure what’s going on

 

Exception in thread Thread-1:

Traceback (most recent call last):

  File "/programs/x86_64-linux/ccpnmr/2.4.2/python2.7/lib/python2.7/threading.py", line 810, in __bootstrap_inner

    self.run()

  File "/programs/x86_64-linux/aria/2.3.1/src/py/aria/JobManager.py", line 193, in run

    f(self)

  File "/programs/x86_64-linux/aria/2.3.1/src/py/aria/JobManager.py", line 331, in job_done

    self.dispatch_job(host)

  File "/programs/x86_64-linux/aria/2.3.1/src/py/aria/JobManager.py", line 337, in dispatch_job

    self.done()

  File "/programs/x86_64-linux/aria/2.3.1/src/py/aria/JobManager.py", line 384, in done

    self.__callback()

  File "/programs/x86_64-linux/aria/2.3.1/src/py/aria/cns.py", line 2662, in <lambda>

    callback = lambda v = vars, f = self.refine_done: f(v)

  File "/programs/x86_64-linux/aria/2.3.1/src/py/aria/cns.py", line 2522, in refine_done

    self.__callback()

  File "/programs/x86_64-linux/aria/2.3.1/src/py/aria/Protocol.py", line 654, in <lambda>

    c = self.structure_calc_done: c(engine, molecule, it)

  File "/programs/x86_64-linux/aria/2.3.1/src/py/aria/Protocol.py", line 624, in structure_calc_done

    ensemble = engine.getEnsemble(it_settings, molecule)

  File "/programs/x86_64-linux/aria/2.3.1/src/py/aria/cns.py", line 666, in getEnsemble

    ensemble.read(pdbfiles, molecule, float_files = swapped_atoms)

  File "/programs/x86_64-linux/aria/2.3.1/src/py/aria/StructureEnsemble.py", line 194, in read

    pdb_dict = self.reader.read(files[j], chain_types, format[j])

  File "/programs/x86_64-linux/aria/2.3.1/src/py/aria/PDBReader.py", line 186, in read

   dict['noe_violations'] = float(data[13:].split(',')[0])

ValueError: could not convert string to float: D1_ApoH3_violations_1.pdb"