VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
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.
http://www.ks.uiuc.edu/Research/vmd/plugins/topotools/

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?

thanks,
    axel.
>
>
>
>
> Thank you in advance
> Sunjoo 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   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.