On Tue, Feb 26, 2013 at 9:10 PM, 吴云剑 <yunjian.wu.hotmail.com> wrote:
>
> Does any one know how VMD display periodic image of an octahedron box? In
> my simulation, my enzyme is on one side of octahedron box and ligand
> molecule on the other side. I assume one is binding with another in
> neighbouring box.
> I've tried "Graphical Representations" -> "Periodic", but it does not show
> correctly.
>
If that doesn't work, I'm not sure what will (if anything). This question
is probably better asked on the VMD mailing list.
One option is to reimage your trajectory using cpptraj. With a fully
up-to-date AmberTools 12, use the "autoimage" command to center your
protein and ligand in the water box.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Feb 26 2013 - 19:00:02 PST
