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.

Giacomo