As the name suggests these are not real atoms. The "multi-center" points I add in Marvin Sketch show up as "dummy atoms" in Avogadro. This is because Avogadro doesn't have multi-center coordination bonds, while Marvin does. However, I build ferrocene using Marvin Sketch and import the structure into Avogadro. 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. The screencast shows how to build two molecules: a model of a zinc finger and a substituted ferrocene. 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. 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.
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