AMBER Archive (2008)

Subject: AMBER: problems with 10-12 potential in amber8 sander

From: Amie Demmel (
Date: Thu Feb 28 2008 - 14:59:27 CST

After pouring through the manual and web searches, I would appriecate any help.
Okay, so I need to use 10-12 LJ potential in amber8 sander for a coarse grain
model developed in my group. So,I have added -DHAS_10_12 to the config.h file
and recompiled with AMBERBUILDFLAGS, as explained in manual. However I get very
strange results.

In order to get sander to read my prmtop file (I am using an oldstyle prmtop) I
had to modify rdparm.f file and "reset" nphb and nptra variables. Both of
these varibles were fine until rdparm read in absol values and then nphb =
1106298783(orig. nphb = 1653) and nptra = 536870912(orig. nptra = 108), these
changes in value caused problems in reading in the rest of the prmtop. Once I
reassigned these varibles(by having program recalculate what they should be),
the problem was corrected. But, when I run a simple minimization( of a 57
residue protein, no explicit water)

      imin=1,maxcyc = 1000,

I get unreasonable energies, stops after 30 steps, and the error message:
" 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"

However, running the same minimization with Sander.5.0.1 the energies are
reasonable, runs to completion, and there is no error message. I would just
use Sander.5.0.1, but I will eventually need to use langevin dynamics in my
simulation runs. Any ideas how I can solve this problem?

Amie Demmel
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