AMBER Archive (2004)

Subject: AMBER: atom out of bounds

From: Venkata S Koppuravuri (kvsuneel_at_linus.bmb.wright.edu)
Date: Wed Jul 21 2004 - 08:25:25 CDT

Hi All,

I am trying to do simulated annealing on a protein structure and i got the
following error.

----------------------
 Frac coord min, max: 0.1637855320600532 1.000268454404591
 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
-----------------------------------

can somebody please explain what this error exactly means.

when I observed the final structure before the simulation stopped one
of the n-terminus is extending almost perpendicularly (in my case i am
expecting the n-terminus to move). If it is because of this n-terminus
going out of the box can someone help me here.

If i have to increase the box size please let me know how to do that.

Thanks in advance

-Venkat

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