AMBER Archive (2008)

Subject: RE: AMBER: nmode "Atom out of bounds" for min of multiple ligands

From: Ross Walker (
Date: Thu May 08 2008 - 12:19:34 CDT

Hi Seth,


I am amazed that you see this error message during minimization since
typically minimization even for a high energy structure only moves things a
short way. It is possible that you have atoms overlapping though and got an
infinite force leading to an infinite displacement but normally this would
crash with some kind of segfault rather than a virtual box error. You
normally see these types of errors during gas phase MD where your system
blows up for example in the first simulation in tutorial B1 where the
double stranded DNA blows apart.


It would be useful to see your actual output.


In addition you are running a gas phase simulation here no implicit
salvation so it is no wonder that the DNA is not stable you probably want
to be using GB during the minimization (igb=5). See the following for an
example of the problems with trying to simulate DNA in a vacuum:


That said I am still amazed this problem occurred during minimization so you
likely have a very bad starting structure you should check for overlaps


Good luck,



From: [] On Behalf Of
Seth Lilavivat
Sent: Thursday, May 08, 2008 7:30 AM
Subject: AMBER: nmode "Atom out of bounds" for min of multiple ligands


Dear Amber Users,

I am using the MM-PBSA method to estimate binding energies. I am also
including entropy calculations using nmode. Everything seems to be working
fine except for one of my systems. I am looking at the binding of various
drugs to DNA. In one of my systems with multiple ligands in a certain
configuration, I am experiencing the following error during the Sander
minimization of nmode.

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

No restart file is generated. It happens when minimizing just the ligands
(no receptor present). It is apparent that it is specific to the arrangement
of the drugs because I am able to successfully minimize ligand coordinates
with other configurations. I am trying to calculate entropy contributions
for complex, receptor, and ligand of a particular system. Am I going about
this the correct way? What can I do to get past this? I have also listed my file:

File generated by
  ntxo = 0,
  ntf = 1, ntb = 0,
  dielc = 1.0,
  cut = 99.0, nsnb = 99999,
  scnb = 2.0, scee = 1.2,
  imin = 1, maxcyc = 20000,
  ncyc = 0, drms = 1.0e-4
  eedmeth= 5,

Thanks always,

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to