VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Feb 27 2012 - 09:19:31 CST

On Mon, Feb 27, 2012 at 10:07 AM, Dimitrios Mantzalis
<dmantzalis_at_gmail.com> wrote:
> Axel,
>
> I had done these steps but the angles, dihedrals etc sections are empty.  My
> problem is that I cannot find a way to keep the topology,or recompute, if I
> have manipulated the geometry by my self first.

you must be doing something wrong. i've been messing
with systems a lot and the core of topotools was written
for that purpose. the problem is, that you always have to
pass all information along. best you don't even write to
an intermediate file. topotools has all the facilities to do
that. OTOH, it also has the facilities to recover angle, dihedral
and improper topology information from the bonding topology.
that is essentially, what the nanotube builder is using.

just go back and read the documentation again and
use some common sense. you should see that it
is all there, it probably just is not written down so
that you can use it without thinking.

axel.

>
> D. 

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