based on the little information youhave given I would suggest running with
iwrap=1.
have you visually inspected the system at the end of the run? what do you
see?
On 6/29/07, Colby C <colbychiauzzi.gmail.com> wrote:
>
> 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 - 06:07:40 PDT
