VMD-L Mailing List

From: Ali Alizadeh (ali.alizadehmoj_at_gmail.com)
Date: Wed Aug 07 2013 - 15:03:10 CDT

Dear Josh and Axel

Thank you for reply, yes you are right but I want to remove by type of
bonds not indx of atoms. There are a lot of bonds in my simulation box.

On Wed, Aug 7, 2013 at 11:58 PM, Josh Vermaas <vermaas2_at_illinois.edu> wrote:

> 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> wrote:
>
>> Yes.
>> --
>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
>> International Centre for Theoretical Physics, Trieste. Italy.
>> ------------------------------
>> *From: * Ali Alizadeh <ali.alizadehmoj_at_gmail.com>
>> *Sender: * owner-vmd-l_at_ks.uiuc.edu
>> *Date: *Wed, 7 Aug 2013 17:33:40 +0430
>> *To: *<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
>
>
> 

-- 
Sincerely
Ali Alizadeh