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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Received on Sun Apr 01 2007 - 06:07:05 PDT
