Generating top file for Zn bound water protein

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Dear Experts,

I generate topol.top using the following command.
gmx pdb2gmx -o prot.gro -ignh -ff charmm36m-lambdadyn -water tip3p -merge all -ldglu -ldhis -ldasp -ldtyr -ldlys -f 1st.gro

But in the toplo.top file there id no bond information beteen ZN atom with the three histidine and one water molecule. In the 1st.gro file I name the ZN bound water as TIP3.

2

Bonds are never written between molecules unless you specify that they should be via specbond.dat entry (and that the force field needs/supports such bonds).