AMBER Archive (2008)

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

From: Seth Lilavivat (
Date: Thu May 08 2008 - 09:30:24 CDT

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,

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