[AMBER] Imaging issue

From: Hira Jabeen <hira_bioinfo.yahoo.com>
Date: Tue, 8 Oct 2019 10:58:06 +0000 (UTC)

Hi everyone,
I am running MD simulations using Amber18-Ambertools 19 with CHARMM forcefield. It seems like my protein complex is moving out of PBC box during simulation.
I tried "autoimage" and also "image with center" within the production run script but coming with the following error: 
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

Here is a piece of Production run Script:
   cat > image.in <<EOF
parm tem1-mem.parm7
trajin md$x.nc
center :1-264 mass origin
image familiar com :1-264
trajout md$x0.nc
    cpptraj < image.in &> image.out
  $MYEXE -O -i md10.i -o md$x.log -p tem1-mem.parm7 -c md$x0.rst -x md$x.nc -r md$x.rst &

But when I run image + center separately on a single coordinate file, it run smoothly without error but the complex blink for several frames and then disappears from the visualizer.
Here is the script: parm tem1-mem.parm7
trajin md10.nc
center :1-264 mass origin
image familiar com :1-264
trajout md10.nc
Please suggest something about this.Thanks,Hira

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Received on Tue Oct 08 2019 - 04:30:02 PDT
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