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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 deepak kumar Wed Feb 15 03:01:14 2012

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]>
> >
> > This message has been automatically forwarded to you by the Adun team
> http://adun.imim.es
> > _______________________________________________
> > Adun-users mailing list
> > [EMAIL PROTECTED]
> > https://mail.gna.org/listinfo/adun-users
>
>


-- 
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
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