VMD-L Mailing List

From: Ali Alizadeh (ali.alizadehmoj_at_gmail.com)
Date: Wed Aug 07 2013 - 16:07:29 CDT

Dear Josh

Thank you very much for your reply.

On Thu, Aug 8, 2013 at 12:45 AM, Josh Vermaas <vermaas2_at_illinois.edu> wrote:

> Bondtypes tend not to be loaded by VMD. What you could do is something
> like this:
>
> topo retypebonds
> foreach bond [topo getbondlist type] {
> puts $bond
> #instead of just printing the bond, what you'd do here is figure out some
> logic to determine if you wanted to keep it or not
> #topo delbond [lindex $bond 0] [lindex $bond 1]
> }
>
> Doing the same thing for angles proceeds similarly.
> -Josh
>
>
> On 08/07/2013 03:03 PM, Ali Alizadeh wrote:
>
> 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
>
>
> 

-- 
Sincerely
Ali Alizadeh