Re: AMBER: Sander error

From: Viktor Hornak <>
Date: Fri, 11 Mar 2005 11:36:38 -0500

Vojtěch Klusák wrote:

> We are calculating a protein in a water sphere, no PBC. During a
> minimization, sander program stops with the following error message.
> Can anyone tell what is the virtual box, fractional coordinates in
> this case and give any hint how to tackle the problem?
This sounds like one of your water molecules flew too far away from the
original water sphere. Did you create your water cap (sphere) in leap?
Do you use ivcap and fcap to control the water cap in your sander input?
One thing which doesn't seem to make sense with regard to my guess of
water flying away, is that it happens during minimization. It just looks
unlikely that water could escape far enough during minimization (unless
there are some serious bad overlaps?). You can check yourself by
carefully looking at the last restart file that was produced in
minimization in some graphical program (VMD or such). Watch carefully if
any water is far away from the original sphere - you may need to zoom
out quite a bit otherwise you may not notice something that's 10A from
your system...


> Frac coord min, max: -1.83733209877266 1.17619196230260
> 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
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Received on Fri Mar 11 2005 - 16:53:00 PST
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