Thank you very much for your answer
Sophie
Quoting Jerome.GOLEBIOWSKI.unice.fr:
> Sophie,
> your system has exploded, probably since your starting structure is too bad.
> the GMAX (maximum gradient) on atom 3817 is very huge.
> This atom has been ejected from the structure.
> Look at your structure on the restrt file, it is probably highly distorted.
> Maybe you sould reconsider your GPCR building procedure.
> Good luck
> Jerome
>
> Selon Sophie Barbe <s)barbe.insa-toulouse.fr>:
>
> >
> >
> > Dear amber users,
> >
> >
> > At the end of the .out file of a minimization of a G protein-coupled
> > receptor,
> > there is :
> >
> > NSTEP ENERGY RMS GMAX NAME NUMBER
> > 9000 -3.0586E+07 1.9085E+11 1.3847E+13 O 3817
> >
> > BOND = 257.3905 ANGLE = 1156.7512 DIHED =
> > 3996.6454
> > VDWAALS = -2575.9535 EEL = ************* HBOND =
> > 0.0000
> > 1-4 VDW = 1189.3758 1-4 EEL = 12856.2338 RESTRAINT =
> > 0.0000
> > Frac coord min, max: -15696926.672801873 15696927.611958483
> > The system has extended beyond
> > the extent of the virtual box.
> > Restarting sander will recalculate
> > a new virtual box with 30 Angstroms
> > extra on each side, if there is a
> > restart file for this configuration.
> > SANDER BOMB in subroutine Routine: map_coords (ew_force.f)
> > Atom out of bounds. If a restart has been written,
> > restarting should resolve the error
> >
> >
> > Could you explain me bu some means?
> >
> > Many thanks by advance
> >
> > Sophie
> >
> >
> >
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>
>
> --
> Jérôme Golebiowski, Ph D.
> Lab CMBA, University of Nice Sophia Antipolis
> 06108 nice cedex 2
> France
> tel: +33 (0)4 92 07 61 03
> http://www.unice.fr/lcmba
> http://www.unice.fr/lcmba/golebiowski
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>
Sophie Barbe
Chercheur Post-doctoral
LISBP- Groupe de Catalyse et Ingenierie Moleculaire Enzymatiques
UMR INSA-CNRS 5504/ UMR INSA-INRA 792
135, avenue de Rangueil
31077 Toulouse cedex 04
France
Tel: +33 (0) 561 559 963
+33 (0) 561 559 273
Fax: +33 (0) 561 559 400
E-mail: sbarbe.insa-toulouse.fr
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Received on Sun Apr 01 2007 - 06:07:05 PDT
