Linear Molecule virtual construction site

I would like to run the MD simulation of a linear molecule and I came to know from the link mentioned below that a virtual construction site should be added in the topology to maintain perfect linearity.
But I am confused that how can I generate the coordinate files (pdb) of such linear molecule using the dummy atoms? Can I able to do with the general software like Avogadro or Gauss view or need to do something else? It will be very helpful if anyone put some light on this.
Thanks in advance.