VMD-L Mailing List

From: Nitin Bhardwaj (nbhardwaj_at_gmail.com)
Date: Tue Oct 25 2005 - 16:09:00 CDT

Hi John,
  I rectified the problem by moving the hydrogen atom a little closer
to the oxygen atom. I can see the bond. Thanks for the help.

Rgds,
Nitin
On 10/24/05, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> Nitin,
> If you use the a22 test version of VMD 1.8.4, you can save a partial PSF
> file that includes bond information, and that way you can reload it again
> later as you describe. Normally you'd already have a PSF file to start with
> and thus your bonds would be correct already. If you don't have a PSF file,
> then writing one out in the newest test version will work for this purpose.
>
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Fri, Oct 21, 2005 at 01:33:00PM -0500, Nitin Bhardwaj wrote:
> > 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
> > >
> > > --
> > > NIH Resource for Macromolecular Modeling and Bioinformatics
> > > Beckman Institute for Advanced Science and Technology
> > > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > > Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> > > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
> > >
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>