# what should do with zink-protein.pdf to get topology file? **URL:** \ **Category:** User discussions\ **Tags:** pdb2gmx, forcefield, mdp-parameters, mdrun, simulation-setup\ **Created:** [September 22, 2025, 9:11am UTC](https://gromacs.bioexcel.eu/t/what-should-do-with-zink-protein-pdf-to-get-topology-file/12676 "2025-09-22T09:11:46Z")\ **Posts on this page:** 6\ **Page:** 1
**Author:** ![sololevel](https://avatars.discourse-cdn.com/v4/letter/s/ce7236/32.png) [@sololevel](https://gromacs.bioexcel.eu/u/sololevel)\ **Post date:** [September 22, 2025, 9:11am UTC](https://gromacs.bioexcel.eu/t/what-should-do-with-zink-protein-pdf-to-get-topology-file/12676/1 "2025-09-22T09:11:46Z")
Hi I have question about getting protein which contain zinc in .gro format by using pdb2gmx command from .pdb, what forcefield should i used? and overall, what should i do when facing a metalloprotein in MD , this is the erro from gmx command: Fatal error: Residue ‘ZN A’ not found in residue topology database thank you ---
**Author:** ![Ashutosh](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/ashutosh/32/2587_2.png) [@Ashutosh](https://gromacs.bioexcel.eu/u/Ashutosh)\ **Post date:** [September 26, 2025, 10:00am UTC](https://gromacs.bioexcel.eu/t/what-should-do-with-zink-protein-pdf-to-get-topology-file/12676/2 "2025-09-26T10:00:25Z")
i have also simulated a protein with zinc and calcium atoms in it. Please check in pdb file how zinc atom is written before processing it pdbgmx TER HETATM 3974 ZN ZN X 1 34.172 52.591 45.051 1.00 31.31 Zn HETATM 3975 ZN ZN X 2 25.832 43.383 46.544 1.00 41.28 Zn HETATM 3976 CAL CAL X 3 28.245 45.566 35.450 1.00 26.00 Ca HETATM 3977 CAL CAL X 4 31.964 36.473 34.570 1.00 61.23 Ca ---
**Author:** ![sololevel](https://avatars.discourse-cdn.com/v4/letter/s/ce7236/32.png) [@sololevel](https://gromacs.bioexcel.eu/u/sololevel)\ **Post date:** [September 30, 2025, 1:09pm UTC](https://gromacs.bioexcel.eu/t/what-should-do-with-zink-protein-pdf-to-get-topology-file/12676/3 "2025-09-30T13:09:53Z")
Unfortunately, it doesn’t make .gro file ATOM 657 HZ1 LYS A 63 10.932 -3.318 -3.781 1.00 3.01 H ATOM 658 HZ2 LYS A 63 10.619 -1.695 -4.109 1.00 2.95 H ATOM 659 HZ3 LYS A 63 12.032 -2.130 -3.279 1.00 2.96 H TER HETATM 660 ZN ZN X 101 1.856 -0.514 -1.076 1.00 0.43 Zn ---
**Author:** ![Ashutosh](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/ashutosh/32/2587_2.png) [@Ashutosh](https://gromacs.bioexcel.eu/u/Ashutosh)\ **Post date:** [October 1, 2025, 2:46pm UTC](https://gromacs.bioexcel.eu/t/what-should-do-with-zink-protein-pdf-to-get-topology-file/12676/4 "2025-10-01T14:46:07Z")
can you print the error here, what it says and also please share the screenshot of last part of your pdb file where this zn atom is written ---
**Author:** ![sololevel](https://avatars.discourse-cdn.com/v4/letter/s/ce7236/32.png) [@sololevel](https://gromacs.bioexcel.eu/u/sololevel)\ **Post date:** [October 7, 2025, 5:51pm UTC](https://gromacs.bioexcel.eu/t/what-should-do-with-zink-protein-pdf-to-get-topology-file/12676/5 "2025-10-07T17:51:55Z")
[Protein\_zink.txt](https://gromacs.bioexcel.eu/uploads/short-url/zZMmfgtxZCrGqXM7dLZ6b1OeMDb.txt) (50.5 KB) Thanks for your consideration. This is my processed protein with a zinc atom. When I ran pdb2gmx command as I mentioned above, I encountered an error. ---
**Author:** ![sololevel](https://avatars.discourse-cdn.com/v4/letter/s/ce7236/32.png) [@sololevel](https://gromacs.bioexcel.eu/u/sololevel)\ **Post date:** [October 7, 2025, 5:54pm UTC](https://gromacs.bioexcel.eu/t/what-should-do-with-zink-protein-pdf-to-get-topology-file/12676/6 "2025-10-07T17:54:27Z")
> [@sololevel](#): > > Fatal error: > Residue ‘ZN A’ not found in residue topology database Fatal error: Residue ‘ZN A’ not found in residue topology database