this simply means your input script has a problem. Do one thing
Before running sander,
define a box out of your protein having charge 0.
Then run the input script.
What is your input script by the way. It has some boundary parameters,
not matching with other mentioned constraint parameters. Have you used
ntb?
Just give the script.
Ashish Runthala
On Sun, Aug 2, 2009 at 11:52 AM, bharat lakhani<lakhbharat.gmail.com> wrote:
> When i am minimizing my system by sander.It showing error like
> following.what does it mean.what i have to do.
>
> Frac coord min, max: -923749.038795444 923750.106780641
> 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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>
--
Ashish Runthala,
Faculty Division III,
Lecturer, Biological Sciences,
Birla Institute of Technology and Science,
Pilani, Rajasthan- 333031
INDIA
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Received on Wed Aug 19 2009 - 20:13:17 PDT
