Residue ZN401 has type ‘Ion’, assuming it is not linked into a chain?

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GROMACS version: 2020
GROMACS modification: Yes/No
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My complex has ZN, DNA, RNA and protein
in the PDB I have the LINK section which includes all the links between ZN ions and DNA
I got this note when I used pdb2gmx
Residue ZN401 has type ‘Ion’, assuming it is not linked into a chain.
Problem with chain definition or missing terminal residues
This chain does not appear to contain a recognized chain molecule

I am not sure if that is a problem or no? all advice are appreciated

my second question is how to add the distance restrain on zn ions?

Thank you very much

2

Hi,

For distance restraints, a section of [ bonds ] type 6 can be used to apply individual restraints between pairs of atoms, see Topology file.

Best regards
Alessandra