Hi Jason,
Thanks for your reply. It is still showing the same problem. I think there
is something wrong with my VMD visualizer then. I guess this error is
related to VMD installed in my system.
I have cross checked it in another system as well.
Thanks a ton Jason,
Regards,
Hirdesh
On Tue, Jan 25, 2011 at 3:59 PM, Adrian Roitberg <roitberg.qtp.ufl.edu>wrote:
> Have you tried loading this pdb into vmd ?
> There is nothing wrong with it as far as I can tell.
> It visualizes perfectly fine in my system.
>
> My guess is that the 'artifact' you saw is related to loading the
> prmtop/crd combo into vmd using the wrong file types. You need to load
> the crd from amber as crdbox.
>
> Cheers
> a.
>
>
> On 1/25/11 11:22 AM, Hirdesh Kumar wrote:
> > 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
> >> _______________________________________________
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> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> >
> >
> > _______________________________________________
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>
> --
> Dr. Adrian E. Roitberg
> Associate Professor
> Quantum Theory Project, Department of Chemistry
> University of Florida
>
> Senior Editor. Journal of Physical Chemistry.
>
> on Sabbatical in Barcelona until August 2011.
> Email roitberg.ufl.edu
>
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Received on Tue Jan 25 2011 - 03:30:04 PST
