Hi Oliver,
Yes I did it correctly. Actually even when I loaded .pdb file in file type
pdb then also it is showing unusual bonds in water. I think it was related
to improper installation of VMD as in another computersystem, in VMD it is
loaded correctly.
The issue is resolved now.
Thanks,
Hirdesh
On Tue, Jan 25, 2011 at 5:40 PM, Oliver Grant <olivercgrant.gmail.com>wrote:
> 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
> > > >>> _______________________________________________
> > > >>> AMBER mailing list
> > > >>> 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
> > > >> AMBER.ambermd.org
> > > >> http://lists.ambermd.org/mailman/listinfo/amber
> > > >>
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > 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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> > >
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> >
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>
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Received on Tue Jan 25 2011 - 04:30:06 PST
