Can you attach your PDB? This is very strange behavior.
On Tue, Jan 25, 2011 at 1:12 AM, Hirdesh Kumar <hirdesh.iitd.gmail.com>wrote:
> Hi,
> I prepared my protein using tleap, solvated it in truncated octahedron
> using
> TIP3P watertype. But when I tried to visualize it using VMD the protein is
> showing outside the waterbox. Is it some visualization problem or I have
> not
> prepared the waterbox correctly.
> Below mentioned is the commands which I used to solvate my protein.
>
> solvateoct com TIP3PBOX 10.0
>
>
> Here I want to add, when I developed the .pdb file and visualize it. In VMD
> it is showing same unusual bonds and protein outside the waterbox. Same pdb
> file in the pymol seems ok.
> Is it limitation of VMD or there is something wrong with my protein
> structure?
>
>
> Please give me your suggestion on this.
>
> Thanks,
> Hirdesh
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Mon Jan 24 2011 - 22:30:05 PST
