From: Jiajian Li (
Date: Wed Jan 18 2012 - 16:01:10 CST

Dear All:

      When I was using VMD Parameterization Tool to develop the CHARMM ff
parameter for a metal complex ( FE as core atom, *attached* ) in our
protein, I was confused in following situation:

1) load targeted PDB file as "base molecule" in the Paratool Main.

2) Go to "Edit -> Metal complexes/FeS-clusters -> Use imidazole for
histidine ligands".

      Then I found that many ligands recognized as "Ligands" by
VMD disappeared, and some atoms that shouldn't be recognized as "Core
atoms" appears in such field.

      Could someone who's an expert or familiar with this part of code in
VMD please indicate me why there's such a problem and how can I fix it? And
thanks so much!