AMBER Archive (2009)

Subject: RE: [AMBER] please help me out

From: Ross Walker (
Date: Wed Apr 08 2009 - 10:34:51 CDT

Hi Bharat,

You are running a gas phase simulation. This means one of two things have
occurred. The first is that your system may have blown up because it is
unstable in a vacuum at 300K like most proteins are in reality. The second
is that your system has diffused too far away from the origin which it will
do in gas phase if you don't remove center of mass rotation and translation.

However, the strange thing is that your input file suggests you are doing a
minimization and I have never seen this error before for a minimization
since this typically doesn't change the coordinates much. My guess though is
that either this is not the input file you used or your initial system is
really high in energy due to the structure being bad. You should probably
start with this.

Good luck,

-----Original Message-----
From: [] On Behalf
Of bharat lakhani
Sent: Wednesday, April 08, 2009 2:19 AM
To: AMBER Mailing List
Subject: [AMBER] please help me out

respected sir,
                      when i am running sander.I am getting following error

 Frac coord min, max: -125660551.867471 125660552.914482
 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

For minimization i am giving these parameters

in vacuo minimization
  imin = 1,
  maxcyc = 1000,
  ncyc = 200,
  ntb = 0,
  igb = 0,
  cut = 12
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