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Re: [Adun-users] Fwd: Detail - Name NSInternalInconsistencyException. Reason Torsion evaluation was not successful. Some atoms were invalid, most probably due to an exploding simulation Michael Johnston Wed Feb 15 04:00:37 2012

Firstly, what relation, if any, does this problem have with the 'Unexpected
exception' problem?

For the specific files in the drop-box the probelm is due to the previously
mentioned torsion/exploding simulation - there is excessive strain still in
the starting structure as described by the initial energetics in the log
file

System: The_GUY_new
                       1-4Coulomb: -405.08847 kcal/mol
                           1-4VDW:   63.75664 kcal/mol
             CoulombElectrostatic: -338.39762 kcal/mol
                   FourierTorsion: 66380.58123 kcal/mol
                    HarmonicAngle: 55586.83031 kcal/mol
                     *HarmonicBond: 44089462.42522 kcal/mol*
          HarmonicImproperTorsion:  719.92989 kcal/mol
            TypeTwoVDWInteraction:   -9.54922 kcal/mol

As Jordi suggested check the atoms in reported torsion in the input
structure - more minimisation is probably necessary.

In addition you can extract a datasource for the last-frame of the
minimisation (either in the GUI or using Scripts/GetLastSnapshot.st) and
use SystemAnalysis plugin to analyse it.

2012/2/15 deepak kumar <[EMAIL PROTECTED]>

> Sorry ...for the previous email..the files can be found in Dropbox..I have
> invited adun users to view it..also here is the link
>
> https://www.dropbox.com/home/Adun#:::101362463
>
> Thanks.
>
> On Wed, Feb 15, 2012 at 11:36 AM, Jordi Villà i Freixa <
> [EMAIL PROTECTED]> wrote:
>
> > you cannot attach files to the list. Please, create a dropbox folder with
> > the material and send the link
> >
> > On Feb 15, 2012, at 11:35 AM, deepak kumar wrote:
> >
> > > Hi,
> > >
> > > All input files and output files are attached.
> > >
> > > Explicitsolvent_AdunCore.errors, Explicitsolvent_AdunCore.log : files
> > > obtained after simulation
> > >
> > > Explicitsolvent_2kxnB.pdb : file obtained from the trajectory of
> > simulation
> > > using Resultconverter.
> > >
> > > Minimisation_AdunCore.errors, Minimisation_AdunCore.log : files
> obtained
> > > after minimisation
> > >
> > > Minimisation_2kxnB.pdb : file obtained from the trajectory of
> > minimisation
> > > using Resultconverter.
> > >
> > > 2kxnB_adun_reduce_fixed.pdb : pdb file used for creating the
> > > system(datasource file)
> > >
> > > template_withxleap.temp : template file
> > >
> > > The_GUY_new.datasource : datasource file
> > >
> > > minimisationsteepestdescent.temp : minimisation file.
> > >
> > > Thanks.
> > >
> > > ---------- Forwarded message ----------
> > > From: deepak kumar <[EMAIL PROTECTED]>
> > > Date: Tue, Feb 14, 2012 at 5:50 PM
> > > Subject: Detail - Name NSInternalInconsistencyException. Reason Torsion
> > > evaluation was not successful. Some atoms were invalid, most probably
> due
> > > to an exploding simulation
> > > To: adun-users <[EMAIL PROTECTED]>
> > >
> > >
> > > Hi ,
> > >
> > >
> > > In addition to the previous email , I ran the simulation again and the
> > > attached files are the output of the run. Minimization_2kxnB.pdb is the
> > > file obtained after minimization.It contains only RNA and no
> protein(Plz
> > > have a look)?? The original PDB file "2kxnB_adun_reduce_fixed.pdb" has
> > both
> > > Protein and RNA, reduced and fixed by "Add Hydrogens" plugin of Adun
> and
> > > "repairpdb.py" program.  As compared to previous trajectories obtained
> > > after simulation and minimization, this trajectory pdb files have only
> > RNA
> > > and protein is missing. If you could plz have a look?
> > >
> > > The aduncore error files say this error.. Also, I would like to mention
> > (I
> > > dont know if it's relevant), Aduncore error files say "Amber99SB"
> > > forcefield being used and Aduncore.log files say "Amber96".
> > >
> > >
> > >
> > >
> > > 2012-02-14 13:27:39.673 AdunCore[729] Replaced coordinates of system
> > > The_GUY_new with those from link
> > > 2012-02-14 13:27:39.674 AdunCore[729] Replaced velocties of system
> > > The_GUY_new with those from link
> > > 2012-02-14 13:27:39.984 AdunCore[729] Replaced coordinates of system
> > > H2OContainer with those from link
> > > 2012-02-14 13:27:40.047 AdunCore[729] Replaced velocties of system
> > > H2OContainer with those from link
> > > 2012-02-14 13:27:42.538 AdunCore[729] Arena : 186.828125 MB. Hblks :
> > > 545.761719 MB. Uordblocks 65.012817 MB. Fordblocks 121.815308 MB
> > > Processing link {simulation =
> SimulationOutput/Minimisation1.simulation;
> > }
> > > AdAmberTorsion - ERROR
> > > Angle nan. Period 0.155556
> > > Cosine nan. Numerator nan. Denominator nan
> > > Atoms 2 5 24 30
> > > Force constant 0.000000. Phase 0.052360
> > > -10.251388   6.197752     6.272148
> > > 257.753862   91.896335    -25.019792
> > > -7.802546    4.378174     5.248017
> > > nan          nan          nan
> > > 2012-02-14 13:27:49.036 AdunCore[729]
> > > 2012-02-14 13:27:49.036 AdunCore[729] Logging error from domain
> > > AdunKernel.ErrorDomain
> > > 2012-02-14 13:27:49.036 AdunCore[729] Error code 0
> > > 2012-02-14 13:27:49.036 AdunCore[729] Description - Caught an exception
> > > from framework
> > > 2012-02-14 13:27:49.036 AdunCore[729] Detail - Name
> > > NSInternalInconsistencyException. Reason Torsion evaluation was not
> > > successful. Some atoms were invalid, most probably due to an exploding
> > > simulation which occured in an earlier step. Aborting.
> > > 2012-02-14 13:27:49.036 AdunCore[729] Recovery suggestion - User info
> > (nil)
> > > 2012-02-14 13:27:49.339 AdunCore[729] Detected error at top level -
> > > Simulation exiting
> > > 2012-02-14 13:27:49.340 AdunCore[729] Error details follow
> > > 2012-02-14 13:27:49.340 AdunCore[729]
> > > 2012-02-14 13:27:49.340 AdunCore[729] Logging error from domain
> > > AdunKernel.ErrorDomain
> > > 2012-02-14 13:27:49.340 AdunCore[729] Error code 0
> > > 2012-02-14 13:27:49.340 AdunCore[729] Description - Caught an exception
> > > from framework
> > > 2012-02-14 13:27:49.340 AdunCore[729] Detail - Name
> > > NSInternalInconsistencyException. Reason Torsion evaluation was not
> > > successful. Some atoms were invalid, most probably due to an exploding
> > > simulation which occured in an earlier step. Aborting.
> > > 2012-02-14 13:27:49.340 AdunCore[729] Recovery suggestion - User info
> > (nil)
> > > 2012-02-14 13:27:51.451 AdunCore[729] Detected error at top level -
> > > Simulation exiting
> > > 2012-02-14 13:27:51.451 AdunCore[729] Error details follow
> > > 2012-02-14 13:27:51.451 AdunCore[729]
> > > 2012-02-14 13:27:51.451 AdunCore[729] Logging error from domain
> > > AdunKernel.ErrorDomain
> > > 2012-02-14 13:27:51.451 AdunCore[729] Error code 0
> > > 2012-02-14 13:27:51.451 AdunCore[729] Description - Caught an exception
> > > from framework
> > > 2012-02-14 13:27:51.451 AdunCore[729] Detail - Name
> > > NSInternalInconsistencyException. Reason Torsion evaluation was not
> > > successful. Some atoms were invalid, most probably due to an exploding
> > > simulation which occured in an earlier step. Aborting.
> > > 2012-02-14 13:27:51.451 AdunCore[729] Recovery suggestion - User info
> > (nil)
> > >
> > >
> > > Plz let me know if I am getting wrong in the process..
> > >
> > >
> > > Thanks .
> > >
> > >
> > > --
> > > Deepak Kumar
> > >
> > >
> > >
> > >
> > > --
> > > Deepak Kumar
> > > Bioinformatics Laboratory
> > > Institute of Molecular Biology and Biotechnology
> > > Adam Mickiewicz University
> > > Umultowska 89, 61-614 Poznan, Poland
> > >
> > > Phone: +48 66 46 82950
> > > E-mail: [EMAIL PROTECTED] , [EMAIL PROTECTED] <[EMAIL PROTECTED]
> %20>
> > >
> > > This message has been automatically forwarded to you by the Adun team
> > http://adun.imim.es
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> >
> >
>
>
> --
> Deepak Kumar
> Bioinformatics Laboratory
> Institute of Molecular Biology and Biotechnology
> Adam Mickiewicz University
> Umultowska 89, 61-614 Poznan, Poland
>
> Phone: +48 66 46 82950
> E-mail: [EMAIL PROTECTED] , [EMAIL PROTECTED] <[EMAIL PROTECTED]>
>
> This message has been automatically forwarded to you by the Adun team
> http://adun.imim.es
> _______________________________________________
> Adun-users mailing list
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