GROMACS version:2025.0
GROMACS modification: Yes/No
i have Gallium ions in pdb
”HETATM 6170 GA3P GA3P B 800 8.825 5.077 -6.869 1.00 0.00 Ga
HETATM 6171 GA3P GA3P B 900 8.449 6.450 -4.094 1.00 0.00 Ga”
but when i construct the topology it automatically delete my another metal ions.
rocessing chain 2 (2 atoms, 1 residues)
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-jul2022.ff/aminoacids.arn
Checking for duplicate atoms…
Now there are 1 atoms. Deleted 1 duplicates.
Generating any missing hydrogen atoms and/or adding termini.
Now there are 1 residues with 1 atoms
Can someone explain or help on this? Thanks! how can we correctly deal with protein-metal interactions?