Error in creating topology for metalloprotein

User discussions
1

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.

2

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.

3

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