VMD-L Mailing List

From: Germain Salvato Vallverdu (germain.vallverdu_at_univ-pau.fr)
Date: Thu Jan 27 2011 - 14:31:08 CST

Hi

I did what you said about topo plugins. It works perfectly. I opened the
tk console and type topo addbond num1 num2 ect ... . I understand that
step. After that in the main window I saved the state, but topology
information are not in that file.

Actually, I thought that I could have do a specific view, then save the
state of that view in a .vmd file and then modified a little bit that
file with a script in order to get, each time I open vmd, the same view
with right bonds. Is it a way to do that ?

In previous mail you speak about a .psf file which contains topology
information. I look at the .psf files in the protein folder which comes
with vmd. It seems to be easy to write a .pdf or .xyz file and a .psf
file for my system and to load both of them in vmd with a right command.
Do you think that doing this may be a solution ?

Thanks again

Germain

-------- Message initial --------
De: M.Raviprasad <M.Raviprasad_at_my.ndsu.edu>
À: Germain Vallverdu <germain.vallverdu_at_univ-pau.fr>
Cc: vmd-l <vmd-l_at_ks.uiuc.edu>
Sujet: RE: vmd-l: How can I add bonds ?
Date: Wed, 26 Jan 2011 18:15:29 +0000

Hi

You DO NOT need to write scripts If you use topotools plugin

I think you never used topotools Plugin. Based on that assumption I write this:

1] open VMD and load your coordinate file
2] Go to "Extensions" menu bar
3] In that, open "Tk console"
4] In that window type "topo"

you will have topotools information...... PLEASE CAREFULLY READ THAT.... before using that.

As Axel said .....If you want to add a bond between atoms 1 and 2 then you have to type "topo addbond 1 2 "

By using this topotools you can create BONDS , ANGLES, DIHEDRALS etc

THE BEST WAY IS TO READ TOPOTOOLS :http://www.ks.uiuc.edu/Research/vmd/plugins/topotools/

Thanks
M.Raviprasad

________________________________________
From: owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] on behalf of Axel Kohlmeyer [akohlmey_at_gmail.com]
Sent: Wednesday, January 26, 2011 10:02 AM
To: Germain Vallverdu
Cc: vmd-l
Subject: Re: vmd-l: How can I add bonds ?

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.
-- 
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