AMBER Archive (2008)

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

From: Seth Lilavivat (
Date: Thu May 08 2008 - 15:01:45 CDT

Hey Ross,

Thanks for taking a look. There is no overlap and the structure isn't bad.
Remember I am not minimizing DNA but just 3 intercalators by themselves.
They are positively charged so my guess is that they fly apart due to charge

Using GB mimimization does take care of this issue but now I get different
energies than with nmode minimization. This results in the RMSD of the
conjugate gradient being greater than my specified tolerace because E-EEL14
for sander and nmode don't match up. So this brings me to my question: how
do I minimize multiple ligands for using in nmode?


On Thu, May 8, 2008 at 1:19 PM, Ross Walker <> wrote:

> 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 etc.
> Good luck,
> Ross
> *From:* [] *On
> Behalf Of *Seth Lilavivat
> *Sent:* Thursday, May 08, 2008 7:30 AM
> *To:*
> *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
> &cntrl
> 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
> &end
> &ewald
> eedmeth= 5,
> &end
> Thanks always,
> Seth

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