VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Feb 27 2012 - 08:07:24 CST

On Mon, Feb 27, 2012 at 7:55 AM, Dimitrios Mantzalis
<dmantzalis_at_gmail.com> wrote:
> Dear All,
>
> If someone uses the nanotube bulider to create a cnt and then directly uses
> the topotools to convert it to lammps data , the information that it it
> written is full (atoms, bonds, angles, dihedrals, impropers). However, in my
> case, I want to create a CNT-graphene system (so to connect them). So I
> create each structure separately (modify them-for example create a hole in
> the graphene sheet) and then I combine them. My problem is that I cannot
> find a type file (or a way) so when I use the topotools, in the combined
> geometry, to produce the lammps data file it prints only the bonds.  Is
> there any way to add the angles, dihedrals etc through vmd because from what
> I read in the very helpful tutorial concerning topotools that Axel wrotes, I
> have not found something.

you can use a combo of .pdb and .psf files as shown here:

http://sites.google.com/site/akohlmey/software/topotools/topotools-tutorial---various-tips-tricks#TOC-Combine-multiple-data-files-with-ov

axel.

>
> Regards
> Dimitris 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science and Technology
Temple University, Philadelphia PA, USA.