VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Wed Aug 07 2013 - 14:28:46 CDT

Its laid out fairly straightforwardly in the manual for topotools
(http://www.ks.uiuc.edu/Research/vmd/plugins/topotools/) as to what is
all possible. topo delbond is what you want, and you just need to know
the two atom ids.
-Josh Vermaas

On 08/07/2013 12:42 PM, Ali Alizadeh wrote:
>
> Dear Axel,
>
> Thank you for your reply.
>
> Can you enlighten some of aspects? I can recognize and build a list of
> all bonds but I do not know how can I
>
> remove some especial bonds from this list.
>
>
>
> On Wed, Aug 7, 2013 at 6:40 PM, Axel Kohlmeyer <akohlmey_at_gmail.com
> <mailto:akohlmey_at_gmail.com>> wrote:
>
> Yes.
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com <mailto:akohlmey_at_gmail.com>
> http://goo.gl/1wk0
> International Centre for Theoretical Physics, Trieste. Italy.
> ------------------------------------------------------------------------
> *From: * Ali Alizadeh <ali.alizadehmoj_at_gmail.com
> <mailto:ali.alizadehmoj_at_gmail.com>>
> *Sender: * owner-vmd-l_at_ks.uiuc.edu <mailto:owner-vmd-l_at_ks.uiuc.edu>
> *Date: *Wed, 7 Aug 2013 17:33:40 +0430
> *To: *<vmd-l_at_ks.uiuc.edu <mailto:vmd-l_at_ks.uiuc.edu>>
> *Subject: *vmd-l: Considering special bonds not all of bonds,
>
>
> Dear All users
>
> I have three bond types in my simulation box. I want to make a
> system.data file from my pdb.file
>
> so that it includes just one of my three bonds and I should do
> this for angles, too. Are there any
>
> methods in topo tools plugin for this intention?
>
> --
> Sincerely
>
> Ali Alizadeh
>
>
>
>
> --
> Sincerely
>
> Ali Alizadeh