# Error in creating topology for metalloprotein

**URL:** <https://gromacs.bioexcel.eu/t/error-in-creating-topology-for-metalloprotein/681>\
**Category:** User discussions\
**Created:** [August 18, 2020, 9:50am UTC](https://gromacs.bioexcel.eu/t/error-in-creating-topology-for-metalloprotein/681 "2020-08-18T09:50:59Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![fahila](https://avatars.discourse-cdn.com/v4/letter/f/b5e925/32.png) [@fahila](https://gromacs.bioexcel.eu/u/fahila)\
**Post date:** [August 18, 2020, 9:50am UTC](https://gromacs.bioexcel.eu/t/error-in-creating-topology-for-metalloprotein/681/1 "2020-08-18T09:50:59Z")

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GROMACS version: 5.1.4  
GROMACS modification: Yes/ **No**  
Hi,  
I’m trying to built a topology for a protein containing a zinc ion.  
Here is the entry of the ion in the pdb input file:  
ATOM 4872 ZN ZN A 616 53.141 68.638 31.204 1.00 53.98

I’m using 54a7 ff, in which there is a zinc ion group in the aminoacid.rtp file:  
[ZN2+]  
[atoms]  
ZN ZN2+ 2.00000 0  
[bonds]  
[angles]  
; ai aj ak gromos type  
[impropers]  
; ai aj ak al gromos type  
[dihedrals]  
; ai aj ak al gromos type

I’ve tried changing the name of the ZN group (ZN, ZN2+ etc…) but I always get an error message:  
Residue ‘ZN’ not found in residue topology database.

All solution online (including this forum) don’t apply specifically to my problem since a zinc ion is not some unusual ligand and it does appear in the ff files.  
Would love some help.

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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:** [August 18, 2020, 1:07pm UTC](https://gromacs.bioexcel.eu/t/error-in-creating-topology-for-metalloprotein/681/2 "2020-08-18T13:07:53Z")

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The residue in the PDB file is ZN, but your `.rtp` entry is for ZN2+. Hence ZN is not found. Change the `.rtp` entry to ZN and it will work.

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<div class="post-metadata">

**Author:** ![fahila](https://avatars.discourse-cdn.com/v4/letter/f/b5e925/32.png) [@fahila](https://gromacs.bioexcel.eu/u/fahila)\
**Post date:** [August 19, 2020, 6:24am UTC](https://gromacs.bioexcel.eu/t/error-in-creating-topology-for-metalloprotein/681/3 "2020-08-19T06:24:55Z")

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I can’t believe I didn’t think about it…  
It worked perfectly. Thank you!