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
>>
>
>
>
>
>
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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 - 03:00:04 PST
