VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Jan 26 2011 - 10:02:42 CST

On Wed, Jan 26, 2011 at 9:57 AM, Germain Vallverdu
<germain.vallverdu_at_univ-pau.fr> wrote:
> 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 ?

i am confused. i already gave you an example
for exactly that kind of thing in my response email.

outside of that, there is the VMD documentation (user guide and tutorials):
http://www.ks.uiuc.edu/Research/vmd/current/docs.html

what else do you need?

axel.

>
> 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.
> 

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