We are trying to minimize 5 ligands in protein . The minimization in
SANDER works for just the protein but when we run SANDER with the
ligands we get this error
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
Here is out .in file for SANDER
&cntrl
imin = 1,
maxcyc = 500,
ncyc = 250,
ntb = 0,
igb = 0,
cut = 12
/
We think the error is not in the .inpcrd or the .prmtop files.
thanks
On 6/29/07, Ross Walker <ross.rosswalker.co.uk> wrote:
> A fractional coordinate error should not occur with periodic boundaries -
> this is from a gas phase or implicit solvent simulation. They likely have
> two atoms sitting very close or on top of each other and they have flown off
> at close to the speed of light. Note the coordinates 10^7 angstroms!!!
>
> Setting ntwx=1 and running 100 steps and then visualizing the mdcrd file
> should be sufficient to locate the origin of the problem. If the user had
> posted more information, such as energy output, details of their input, the
> type of simulation they were running etc it might have been easier to help.
>
> > another possibility is that you are not using "iwrap", so
> > some particles
> > have moved so far they have existed the bounding box.
> >
> > phin.
> >
> >
> > Colby C schrieb:
> > > Frac coord min, max: -2.0586063485058166E+7 2.058606450492667E+7
> > > 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
> > >
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Received on Sun Jul 01 2007 - 06:07:38 PDT
