Re: [AMBER] Fwd: Query regarding unusual water box in vmd

From: Hirdesh Kumar <hirdesh.iitd.gmail.com>
Date: Tue, 25 Jan 2011 15:52:32 +0530

Hi Jason,
Here I am attaching the pdb file for your reference.

On Tue, Jan 25, 2011 at 11:50 AM, Jason Swails <jason.swails.gmail.com>wrote:

> 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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
>



-- 
##################################
Hirdesh Kumar
PhD Scholar
School of Biological Sciences, IITD
(http://www.iitd.ac.in/bioschool.html)
####################################



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Received on Tue Jan 25 2011 - 02:30:07 PST
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