VMD-L Mailing List

From: Josh Vermaas (joshua.vermaas_at_gmail.com)
Date: Tue Sep 15 2020 - 15:12:00 CDT

Hi,

topotools is available on github and elsewhere, and the code actually isn't
that bad. https://github.com/akohlmey/topotools/blob/master/topobonds.tcl The
code is just an interface to "mol bondsrecalc", as is indicated by the
comment and the code itself. It depends on the atomic radii, and creates a
bond if the distance between the two atoms is less than the sum of the
radii.

-Josh

On Tue, Sep 15, 2020 at 1:05 PM omid gh <molecular.simulator_at_gmail.com>
wrote:

>
> Hi
> does anybody know the algorithm topo tool uses to guess bonds between
> atoms?
> thanks.
> omid.
>