VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Sep 15 2020 - 19:07:28 CDT

whatever happened to reading the documentation?
https://sites.google.com/site/akohlmey/software/topotools/topotools---documentation#TOC-guess-angle-dihedral-s

On Tue, Sep 15, 2020 at 7:41 PM omid gh <molecular.simulator_at_gmail.com>
wrote:

> 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.
>>>
>> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.