VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Oct 24 2005 - 17:20:52 CDT

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