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,
Ross
-----Original Message-----
From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] 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
&cntrl
imin = 1,
maxcyc = 1000,
ncyc = 200,
ntb = 0,
igb = 0,
cut = 12
/
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Received on Fri Apr 10 2009 - 01:09:40 PDT
