what should do with zink-protein.pdf to get topology file?

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1

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

2

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

3

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

4

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

5

Protein_zink.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.

6

Fatal error:
Residue ‘ZN A’ not found in residue topology database