AMBER Archive (2005)

Subject: AMBER: Sander bomb - atom out of bounds

From: Joe Nolan (spaceace13666_at_yahoo.com)
Date: Thu Apr 21 2005 - 12:46:01 CDT

Dear Amber community,
    While attempting a first minimization run in a 10 Angstrom box, the
following error was encountered:

>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

So far I've attempted browsing the archives and scouring the manual for
information on this problem, but have not come about much in the way of
manipulating the molecule to stay within the constraints of the solvent
box. I have a hunch that the solution might lie around centering the
solvent box to the center of mass, but any and all help is greatly
appreciated. Thank you for you time.
-Msgr. E. Joseph Nolan IV

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