AMBER Archive (2004)

Subject: Re: AMBER: minimization output

From: David A. Case (
Date: Tue Feb 10 2004 - 15:05:59 CST

On Tue, Feb 10, 2004, L Jin wrote:
> I got the top and crd file from xleap after running antechamber as before.
> Everything seems fine. But when I ran the following command:
> 'sander -O -i -o min.out -p -c GlcNS.crd -r min.restrt',
> I did not get the min.restrt output file and the min.out contained the following
> message which I never meet before with the same running.
> Frac coord min, max: -0.144743351 1.10900132
> 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

You need to run a short minimization, printing the output every step (ntpr=1).
Somehow, your system is moving by more than 30 Ang upon minimization, which
generally does not happen. Look at the structure at the beginning, and after
10 steps or so, to see which (if any) atoms have moved a long way. You should
also take note of how many steps of minimization you run before seeing the
above message.

...good luck...dac


================================================================== David A. Case | e-mail: Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896 The Scripps Research Institute | phone: +1-858-784-9768 10550 N. Torrey Pines Rd. | home page: La Jolla CA 92037 USA | ================================================================== ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to