This post is long overdue. Quite some time ago (it has been so long I can't find the email anymore) someone asked me to do a post on transition metals.
Modeling of transition metal-containing compounds is notoriously difficult and will require at least two separate posts: one one building the molecules (that's this post) and one on SCF convergence problems.
The screencast shows how to build two molecules: a model of a zinc finger and a substituted ferrocene.
I build the zinc finger model in Avogadro and the only new trick is to pick the UFF force field, because that has parameters for bonds to transition metals.
However, I build ferrocene using Marvin Sketch and import the structure into Avogadro. This is because Avogadro doesn't have multi-center coordination bonds, while Marvin does. The "multi-center" points I add in Marvin Sketch show up as "dummy atoms" in Avogadro. As the name suggests these are not real atoms.
I then use Avogadro to add a functional group to one of the rings and optimize them while leaving the ferrocene part frozen. I could have added the group in Marvin Sketch but Avogadro gives me the opportunity to use autoopt to find the best geometry for the functional group. Note that because I am freezing the transition metal containing part I don't need to assign bonds between the Fe atom and the rings and therefore I can use the MMFF force field, as long as I delete the dummy atoms first.