PBC and topo tool

Hi Axel

I’m going use topo tool for guessing bonds and angles of atoms in a system where some particles cross the pbc and seemingly topo tool cannot guess bonds between periodic images. Am I right?
So, what should I do? Please introduce me a convenient way.

Many thanks in advance.

Hi Robert, since you’re using VMD already it may be useful to use pbc unwrap to bring the coordinates of each pair of to-be-bonded atoms at their nearest-neighbor mutual distance.

If this is not possible, e.g. because you are dealing with a macromolecule that is bonded to one or more of its periodic images, you can use “topo addbond” to manually add bonds for the rest of the TopoTools commands to use.