From: Axel Kohlmeyer (
Date: Wed Jun 05 2013 - 10:42:43 CDT

On Wed, Jun 5, 2013 at 5:22 PM, Ali Alizadeh <> wrote:
> Dear Axel
> Thank you for your reply,
> You are right,
> I was a bit confused, I wanted to define improper dihedrals,
> There isn't any tutorial about it, I do not understand

but there is the documentation.

> Why should we define tolerance for detection of impropers?

you don't need a tolerance to *define* an improper. you can just
define it. there is a command for that. the tolerance is only needed
when trying to *guess*. there is an important difference between the

remember that software cannot do the thinking for you, and topotools
expects that you know what you want *and* check it. it allows to do
things that you cannot do otherwise, but that also means, that you can
easily create a big mess, if you don't know what you are doing.


> --
> Sincerely
> Ali Alizadeh

Dr. Axel Kohlmeyer
International Centre for Theoretical Physics, Trieste. Italy.