From: Peter Freddolino (
Date: Tue Apr 18 2006 - 09:33:19 CDT

Hi Per,
actually, the problem is literally that your topology/parameter files do
not have zinc in them; the "unusual bond" is just a warning because the
distance between protein and the ion is rather short, but this will not
affect psf generation. In this case, the problem is that the residue
name of a single divalent zinc cation should be ZN2, not ZN. You can fix
this by editing your input pdb or running
pdbalias residue ZN ZN2
before you start psf generation.


Per Jr. Greisen wrote:

>I am doing a simulation on a protein having 2 zinc ions; but when I try to
>generate the psf - it gives me the following error:
>unknown residue type ZN
>I think the problem is its coordination with protein because if loaded
>into VMD the it says unusual bond between residue and zinc atom - how to
>fix this?