VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Oct 21 2005 - 12:32:44 CDT

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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