# Generating top file for Zn bound water protein

**URL:** <https://gromacs.bioexcel.eu/t/generating-top-file-for-zn-bound-water-protein/11064>\
**Category:** User discussions\
**Created:** [January 17, 2025, 7:26pm UTC](https://gromacs.bioexcel.eu/t/generating-top-file-for-zn-bound-water-protein/11064 "2025-01-17T19:26:17Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![dulal](https://avatars.discourse-cdn.com/v4/letter/d/fbc32d/32.png) [@dulal](https://gromacs.bioexcel.eu/u/dulal)\
**Post date:** [January 17, 2025, 7:26pm UTC](https://gromacs.bioexcel.eu/t/generating-top-file-for-zn-bound-water-protein/11064/1 "2025-01-17T19:26:17Z")

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GROMACS version:  
GROMACS modification: Yes/No  
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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.

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**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [January 17, 2025, 8:00pm UTC](https://gromacs.bioexcel.eu/t/generating-top-file-for-zn-bound-water-protein/11064/2 "2025-01-17T20:00:35Z")

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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).