[AMBER] Query regarding unusual water box in vmd

From: Hirdesh Kumar <hirdesh.iitd.gmail.com>
Date: Tue, 25 Jan 2011 11:35:38 +0530

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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tleap.png
(image/png attachment: tleap.png)

pymold.png
(image/png attachment: pymold.png)

Received on Mon Jan 24 2011 - 22:30:02 PST
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