AMBER Archive (2004)

Subject: AMBER: minimization output

From: L Jin (s0344557_at_sms.ed.ac.uk)
Date: Tue Feb 10 2004 - 10:36:25 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 min.in -o min.out -p GlcNS.top -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

It seems that something wrong with the box. But actually I did not add any box
for my molecule. I checked the top file it is nearly the same as the one running
minimizaiton well before. Please anybody can give me some suggestion? Thanks in
advance.

Lan

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