From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Wed Aug 07 2013 - 15:15:45 CDT

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
> <mailto: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 <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
>
>
>
>
> --
> Sincerely
>
> Ali Alizadeh