VMD-L Mailing List

From: utku.ozkan_at_bilkent.edu.tr
Date: Wed Nov 09 2022 - 04:29:16 CST

Thank you for fast response,

When I did the commands step by step once again to verify the info you
have asked, I could generate the angle list with guessangles tcl script,
I believe previously I made an error while importing the data to vmd.

Sorry for taking your time due to an error,

Thank you,

Ata Utku Özkan

Bilkent University - UNAM

> 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 $bonds]
> [...]
>
>> As my structure has
>> unusual(long) bonds which "guessbonds" function, previously, could not
>> assign based on atom coordinates and types.
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!5xyzUCa31E8wWCsB6MGwoQZnaooUd9PTbjiTBPhI32WlH0nEN43iGXfMftqPq0EbguMhEQR61IlozLCetXYyGvucKCLC$ [1]
> College of Science & Technology, Temple University, Philadelphia PA,
> USA
> International Centre for Theoretical Physics, Trieste. Italy.

Links:
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[1]
https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!4lr3yW2aSXmYSBItj4yARKSdLet7WT9ZJ_DFpgI72DxadnEwPElQw3_Oq1wCM2K54MOkHhGiDtiIQhlJSQ$