I am using Amber 7 to minimize complex-structure constituted by three
chains (370 Amino acids).
The minimization stops after nstep = 10 and in the file nome.min.out ais
indicated this error:
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.
EWALD BOMB in subroutine Routine: map_coords (ew_force.f)
Atom out of bounds. If a restart has been written,
restarting should resolve the error
Can you help me?
Susan Costantini
> --
>
>
> ...................................................................
> Costantini Susan
> Research Center of Computational and Biotechnological Sciences
> (CRISCEB), Second University of Naples
> Work address:
> Institute of Food Science and Technology - CNR
> via Roma 52 A/C -83100 Avellino (Italy)
> tel:++39.0825.299651 - Fax +39.0825.781585
> mobile: 347/9396453 - 329/5686016
> e-mail:susan.costantini.unina2.it & susan.costantini.isa.cnr.it
> ...................................................................
>
>
>
> --------------6811563BEB029A3E11697D0F
> Content-Type: text/html; charset=iso-8859-15
> Content-Transfer-Encoding: 7bit
>
> <!doctype html public "-//w3c//dtd html 4.0 transitional//en">
> <html>
>
> <br>I am using Amber 7 to minimize complex-structure constituted by three
> chains (370 Amino acids).
> <br>The minimization stops after nstep = 10 and in the file nome.min.out
> ais indicated this error:
> <p>The system has extended beyond
> <br> the extent of the virtual box.
> <br> Restarting sander will recalculate
> <br> a new virtual box with 30 Angstroms
> <br> extra on each side, if there is a
> <br> restart file for this configuration.
> <br> EWALD BOMB in subroutine Routine: map_coords (ew_force.f)
> <br> Atom out of bounds. If a restart has been written,
> <br> restarting should resolve the error
> <p>Can you help me?
> <p>Susan Costantini
> <pre>--
>
>
> ...................................................................
> Costantini Susan
> Research Center of Computational and Biotechnological Sciences
> (CRISCEB), Second University of Naples
> Work address:
> Institute of Food Science and Technology - CNR
> via Roma 52 A/C -83100 Avellino (Italy)
> tel:++39.0825.299651 - Fax +39.0825.781585
> mobile: 347/9396453 - 329/5686016
> e-mail:susan.costantini.unina2.it & susan.costantini.isa.cnr.it
> ...................................................................</pre>
> </html>
>
> --------------6811563BEB029A3E11697D0F--
>
>
>
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Received on Sun Feb 15 2004 - 09:53:00 PST
