From: John Stone (
Date: Wed Feb 01 2012 - 23:21:49 CST

  There were a few bugs in paratool which we have been gradually
trying to get fixed as time goes on. The main developer of paratool
left academia, so it is only getting minor bug fixes now. That said,
it would be useful to know exactly which version of VMD you're running
in order to be able to help more.

  John Stone

On Wed, Jan 18, 2012 at 04:01:10PM -0600, Jiajian Li wrote:
> 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!
> Li

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