From: Josh Vermaas (
Date: Fri Jun 19 2020 - 08:55:59 CDT

Any particular reason why this wouldn't work?

set sel [atomselect top "all"]
$sel get numbonds

That reports the number of bonds attached to each atom. Note however that
from xyz files, VMD guesses bond topologies from the first file loaded, and
never changes them, so if you are coming from a QM trajectory, this won't
do what you likely want to do. In what context do you want to count bonds?


On Fri, Jun 19, 2020 at 4:37 AM Otakandza Glenn <>

> Hi Dear developers,
> I would like to know how to count the number of atomics bonds when viewing
> with VMD for an xyz file.