When loading the top did you select amber7 parm? Then when loading the .crd
file select amber co-ordinates with periodic box.
Oliver
On 25 January 2011 11:12, Hirdesh Kumar <hirdesh.iitd.gmail.com> wrote:
> 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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> > >>>
> > >>
> > >>
> > >>
> > >> --
> > >> 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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> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > --
> > 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 - 04:30:04 PST
