Hello,
It is showing that bond because that bond information is in the prmtop
file... There is a graphical representation called "dynamic bonds"
that will only show bonds within a given distance. You can make it
look very much like the "licorice" representation by using dynamic
bonds with van der waals and reducing the size of the sphere such that
it appears like "licorice".
There may also be another way, but I'm not aware of it.
Good luck!
Jason
On Sat, Jan 23, 2010 at 4:18 AM, mahesh kumar
<kumar.kumarmahesh.mahesh74.gmail.com> wrote:
> Dear Amber Developer
> I had a problem with use of VMD. I loaded with my prmtop using AMBER7 parm
> and mdcrd file using AMBER coordinates with periodic box. I found that one
> bond becomes around 6 angstrom, even that vmd show a bond like a elongated
> bond. what should I do so that vmd shows it like a broken bond and not like
> a elongated bond. One more thing I uses RESP charges calculated using
> Gaussian03.
> Thank you in advance
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>
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Sat Jan 23 2010 - 06:00:04 PST
