Hi Kumar,
Jason is correct here although another option that can work and allows you
to use display settings other than dynamic bonds is to start by loading a
pdb file of your system in place of the prmtop file. You can use ambpdb to
make a pdb file from your prmtop and restart file. Then into the 'molecule'
that gets created by loading the pdb you can load your trajectory file.
Since the pdb file does not have the connectivity data so vmd bonds by
distance and the 6 angstrom bond is not drawn.
That said you say you are using AMBER 7 and do not mention if you are doing
any kind of QM/MM simulation so my suspicion is that something is very wrong
with your simulation. It should not be possible to break that bond so you
likely have a very poor initial geometry or something else wrong with your
simulation / parameters. I would take a careful look at this.
Another problem, if you see lots of these bonds may be that you are loading
a mdcrd file for a periodic system but not telling VMD it contains box
information or vice versa. Check the file format that you are loading the
mdcrd file as. There are two options, with and without box info.
All the best
Ross
> -----Original Message-----
> From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On
> Behalf Of Jason Swails
> Sent: Saturday, January 23, 2010 5:43 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] problem with vmd
>
> 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
> > _______________________________________________
> > 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
>
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Received on Sun Jan 24 2010 - 22:30:04 PST
