AMBER: Sander error

From: Vojtěch Klusák <>
Date: Thu, 10 Mar 2005 13:03:21 +0100

 Dear all,

 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?



 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 Thu Mar 10 2005 - 12:53:00 PST
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