GROMACS version: 2022
GROMACS modification: No
Hi all, I would like to add a copper ion to the force field, with a bonded interaction for S atoms of methionines. I’m a bit confused about what files to edit to achieve this. I copied the amber99sb.ff to a local directory, and edited them to introduce a CU1 ion. Then, I added a CU1 ion to the .pdb file and ran pdb2gmx:
gmx pdb2gmx -f cu_start_test.pdb -o processed.gro -water spce -ff amber99sb
This produces topol_Protein_chain_A.itp and posre_Ion_chain_B.itp, as well as topol.top. I’m unclear as to where to define [ bonds ] of type 6. Since the atoms of the protein and the ion are separated to different topol files, I’m guessing topol.top. However, it’s unclear to me, in that case, how I’d refer to the atom indices, as atoms are numbered separately within each chain file.
The .pdb file looks like this:
...
ATOM 60 2HA GLY A 6 19.298 60.370 27.202 1.00 0.00
ATOM 61 CU1 CU1 B 7 27.616 66.363 28.562 1.00 0.00
END
changing chain B to A results in the following error:
Fatal error:
The residues in the chain GLY2--CU17 do not have a consistent type. The first
residue has type 'Protein', while residue CU17 is of type 'Ion'. Either there
is a mistake in your chain, or it includes nonstandard residue names that have
not yet been added to the residuetypes.dat file in the GROMACS library
directory. If there are other molecules such as ligands, they should not have
the same chain ID as the adjacent protein chain since it's a separate
molecule.
What am I missing?