AMBER Archive (2004)


From: L Jin (
Date: Mon Feb 16 2004 - 07:51:35 CST

Dear all,

 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

 I changed the DIELC value from 1 (default) to 4 then the
failiar vanished for most molecule minimization running. But there are still the
same problem with few others. I am curious how this DIELC affects the running.
Maybe I need to change some basic parameters instead of only this DIELC value.
Any reply would be appreciated. Thanks.


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