From: Axel Kohlmeyer (
Date: Wed May 19 2010 - 06:36:59 CDT

On Wed, May 19, 2010 at 6:18 AM, Narasimhan LOGANATHAN
<> wrote:
> Dear all,
>      I  want to build a zeolite with certain cationic distribution.
> I have built the zeolite but i have to put the cations in a specific location.
> Could anyone let me know is there any way for me to add an atom.
> I know how to move the atom to the specific location but have no
> idea how to add an atom.

VMD is a viewer not an editor. so there is no direct way to add atoms.
what you could do is the following.

first load your zeolithe data and then run these script commands

set numcations 10
package require topotools
set mid [molinto top]
set cat [mol new atoms $numcations]
animate dup $cat
set sel [atomselect $cat all]
$sel set name CAT
$sel delete
set mol [::TopoTools::mergemols "$mid $cat"]

at this point $mol will be the molecule id for a new molecule
that is a copy of your zeolite with 10 atoms added named CAT
and all that is left is to select and position them.


> Thanks in advance
> Regards
> Naresh

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.