From: Axel Kohlmeyer (
Date: Thu Jul 23 2009 - 14:06:53 CDT

On Thu, 2009-07-23 at 13:25 -0500, Sunjoo Lee wrote:
> Hello
> I am trying to draw lipids and other small molecules, which are
> modeled by a coarse-grained model.
> The easiest way seemed to generate a pdb file with the connectivity.
> All the bonding information was given at the end of a pdb file.
> But I still do not see bonds connecting two interaction sites.
> Could anyone tell me what the problem may be and how I can fix this
> problem?

which version of VMD did you try. the recent beta versions should
be able to recognize extra CONECT records and display them, if they
are correctly formatted.

> The second method I would like to try is to use bonding information
> obtained from a gmxdump file.
> Could anyone explain more explicitly how I can use the bonding
> information to draw bonds?

with atom selections you have a getbonds and setbonds command.
those are a bit awkward to use and require some scripting to
reformat the data.

the latest VMD betas have a plugin called topotools that also
allows setting and deleting individual bonds or lists of bonds.

i'd suggest however to check out the file first. if you are
already using the latest beta and still don't see the bonds,
can you post a minimal example that does not work, so that
we can have a look at it and see what is wrong?

> Thank you in advance
> Sunjoo

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.