VMD-L Mailing List

From: omid gh (molecular.simulator_at_gmail.com)
Date: Wed Sep 16 2020 - 04:34:47 CDT

thanks . very helpful

On Wed, Sep 16, 2020 at 4:37 AM Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> 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.
>