From: Germain Vallverdu (germain.vallverdu_at_univ-pau.fr)
Date: Wed Jan 26 2011 - 08:57:30 CST

Thanks this plugins seems to do what I want.

But I did not use to write vmd scripts and I do not know where to start. It will be great if you could give me a short example. For example, suppose that I have a geometry in xyz format and I want to connect atom 1 and 2. How can I write this in a vmd script ?

Thanks

Germain

---------------------------------------------
Germain Vallverdu
Maître de conférences
Université de Pau et des pays de l'Adour
germain.vallverdu_at_univ-pau.fr
05 59 40 78 51
http://gvallver.perso.univ-pau.fr

Le 24 janv. 2011 à 16:58, Axel Kohlmeyer <akohlmey_at_gmail.com> a écrit :

> 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.