GROMACS version: 2025.4-conda_forge
GROMACS modification: No
I am currently conducting simulations on the binding mechanism between a zinc finger protein and a segment of DNA sequence. This zinc finger protein contains nine zinc finger domains that require nine zinc fingers for structural stabilization. My initial structure, predicted by AlphaFold3, consists of a truncated zinc finger sequence (rather than the full-length sequence), the DNA sequence, and nine zinc ions. Afterwards, I ran the most basic command for this structure：
gmx pdb2gmx -f znf263_zf1_9_hs7_c36.pdb -o znf263_zf1_9_hs7_c36.gro -water tip3p -ter -ignh
I chose NH3+ / COO- as the termini for my truncated sequence, yet the log indicates an issue with the processing of my zinc ion chain：
Processing chain 2 'B' (9 atoms, 1 residues)
Residue ZN1 has type 'Ion', assuming it is not linked into a chain.
Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior.
9 out of 9 lines of specbond.dat converted successfully
Opening force field file ./charmm36-feb2026_cgenff-5.0.ff/aminoacids.arn
Checking for duplicate atoms....
Now there are 1 atoms. Deleted 8 duplicates.
Generating any missing hydrogen atoms and/or adding termini.
Now there are 1 residues with 1 atoms
Chain time...
Making bonds...
No bonds
Generating angles, dihedrals and pairs...
Making cmap torsions...
There are 0 dihedrals, 0 impropers, 0 angles
0 pairs, 0 bonds and 0 virtual sites
Total mass 65.370 a.m.u.
Total charge 2.000 e
Writing topology
I don’t know how to handle this?