Dear Community,
I am trying to model a polymer that includes coordination bonds in the backbone (specifically, ferrocene)., and I'm running into two problems (so far). Can anyone help with the following issues?
1. Materials Studio doesn't recognize the coordination bond between the Fe atom and the adjacent cyclopentadienyl (Cp) rings as being part of the polymer backbone, and thus does not recognize the monomer as a valid repeat unit. Is there a way to polymerize monomers containing ferrocene? An example of this polymer is provided below.
2. Another issue seems to be an inability to use the Anneal task in Forcite when a coordination bond is present. When I try to do so, I get the error message: "Dynamics cannot integrate the equation of motion for particles with zero (or small) mass." I understand that the "coordination bond" is a bond between the iron atom and a dummy atom that's centered in the middle of the Cp ring. However, this is a serious problem for the simulations we're trying to run. Is there a way we can model ferrocene while being able to run annealing tasks?
Your help is much appreciated!