VMD-L Mailing List

From: Nitin Bhardwaj (nbhardwaj_at_gmail.com)
Date: Fri Oct 21 2005 - 13:33:00 CDT

hi John,
  Thanks fo replying. I forgot to mention that I had tried the mouse
mode earlier. I could create the and see the bond for the time being.
I saved this PDB file in a new file. When I again load this new file,
I can not again see the bond. Is there another format that I need to
save the structural information in?
Thanks again.
Nitin
On 10/21/05, John Stone <johns_at_ks.uiuc.edu> wrote:
> Hi,
> Until the PDB reader honors CONECT records, you can use the
> Mouse->Add/Remove Bonds mode to do this. If you're preparing
> a simulation, you'd ideally be using a PSF file to specify this
> information anyway, so you'd load that file into the same molecule
> to get the bonds used in the simulation.
>
> John Stone
> vmd_at_ks.uiuc.edu
>
>
> On Fri, Oct 21, 2005 at 12:05:09PM -0500, Nitin Bhardwaj wrote:
> > Hi all,
> > I am trying to create a bond between an oxygen and a hydrogen atom
> > (atom 64 and 65 as follows) in a non-standard lipid.
> >
> > ATOM 64 O10 INO X 2 4.809 -7.607 -1.405 1.00 0.00
> > ATOM 65 H11 INO X 2 4.090 -8.131 -0.074 1.00 0.00
> >
> > so at the end of the PDB file I say:
> >
> > CONECT 64 65
> >
> > But the bond still does not show up in VMD. It shows up fine in PyMol.
> >
> > I think VMD by itself decides whether to place a bond between atoms.
> > The distance between the above two atoms is 1.6 Ang. What do I do to
> > make this bond show up in VMD?
> >
> > I further need to simulate the lipid. Do I need to be worried that
> > this bond does now show up in VMD (although it appears in my topology
> > file that there is bond between O10 and H11?
> >
> > Thanks a lot in advance,
> > Rgds,
> > Nitin
>
> --
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