VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Nov 09 2022 - 03:07:42 CST

Unfortunately, your post leaves out multiple important bits of information
that are needed to give a meaningful answer.
- what version of VMD do you use?
- what version of TopoTools do you use?
- what platform are you running on?
- does this unexpected behavior only happen with this one specific data
file, or also in other cases?
- how exactly do you determine whether angles have been added to your
system or not?
- can you provide the exact sequence of commands that you execute and an
example file to reproduce the issue?

On Wed, Nov 9, 2022 at 1:44 AM <utku.ozkan_at_bilkent.edu.tr> wrote:
[...]

Is it possible that the “guessangles” function utilizes the van der
> Waals radiuses of the atoms to guess the angles?

No.

The following line retrieves the (raw) bond information how VMD stores it
(as a list of bonded atoms with each individual atom) as a list over all
selected atoms (by default all atoms):

   set bonddata [$sel getbonds]

and from here on, the guessangles code loops over all the available bond
data and the atom IDs and atom types to construct topological angles
following the algorithm described in the comment.

    # a topological angle is defined by two bonds that share an atom
    # bound to it that are not the bond itself
    foreach bonds $bonddata aidx $atomindex atyp $atomtypes {
        set nbnd [llength $bonds]
    [...]

> As my structure has
> unusual(long) bonds which “guessbonds” function, previously, could not
> assign based on atom coordinates and types.
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!4lr3yW2aSXmYSBItj4yARKSdLet7WT9ZJ_DFpgI72DxadnEwPElQw3_Oq1wCM2K54MOkHhGiDtiIQhlJSQ$  
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.