From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Jan 24 2011 - 09:58:19 CST

On Mon, Jan 24, 2011 at 10:01 AM, Germain Salvato Vallverdu
<germain.vallverdu_at_univ-pau.fr> wrote:
> Hi all,
>
> When I save a state from VMD the bonds I have added are not recorded.
> How can I write a script where I say to VMD a list of bonds I want to
> create ?

this sounds like a job for the topotools plugin:

http://www.ks.uiuc.edu/Research/vmd/plugins/topotools/

updated versions for VMD 1.8.7 are available from
(the alpha test versions have them already included):
http://sites.google.com/site/akohlmey/software/topotools/

for example:

topo addbond 10 11

will add a bond between atoms with index 10 and 11.
the best way to make this change permanent is to save
the bond information in a psf or similar file and then load
the file in addition of your coordinate files.

cheers,
    axel.

>
> Thanks
>
> Germain
>
>
> --
> Maître de Conférence
> Université de Pau et des pays de l'Adour
> Institut Pluridisciplinaire de Recherche sur l'Environnement et les Matériaux
> Équipe de Chimie Physique
> email  : germain.vallverdu_at_univ-pau.fr
> Tel    : 05 59 40 78 51
> page   : http://gvallver.perso.univ-pau.fr
>
>

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.