Hi,
This error indicates to me that your system might be falling
apart/otherwise unstable.
If you visualize the trajectory it could help determine if this is the case.
Hope this helps,
Christina
On Fri, Sep 18, 2015 at 3:33 PM, Krantzman, Kristin D <KrantzmanK.cofc.edu>
wrote:
> Dear Amber mailing list,
> I am trying to calculate the energy of my solute particle. I stripped the
> trajectory of all solvent and saved the topology file with the option
> nobox. When I try to run sander with imin=5, I get the error "The system
> has extended beyond the extent of the virtual box". I have selected ntb=0
> in my mdin file for input.
> Could you help me figure out what I am doing incorrectly?
> Thank you very much for your help.
> Best, Kristin
>
> Kristin D. Krantzman
> Professor, Department of Chemistry and Biochemistry
> College of Charleston
> Charleston, SC 29424
> (843) 953-3378
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
---------------------------------------------------------------------------------------
Christina Bergonzo, PhD
Postdoctoral Researcher
Department of Medicinal Chemistry, University of Utah
30 South 2000 East, Rm. 201
Salt Lake City, UT 84112-5820
Office: L.S. Skaggs Pharmacy Research Institute, Rm.4290
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652 / Fax: (801) 585-6208
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Received on Fri Sep 18 2015 - 15:00:05 PDT
