VMD-L Mailing List

From: omid gh (molecular.simulator_at_gmail.com)
Date: Tue Sep 15 2020 - 15:22:15 CDT

thanks.
another question what is the algorithm for angle and dihdral and impropers?

On Wed, Sep 16, 2020 at 12:42 AM Josh Vermaas <joshua.vermaas_at_gmail.com>
wrote:

> 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.
>>
>