GROMACS modification: No
I am dealing with a protein containing Zn and K ions. I have used amber99sb-ildn with modified Zn parameters. when i try to generate .gro file using pdb2gmx the following error appears:
The residues in the chain LEU14–K403 do not have a consistent type. The first
residue has type ‘Protein’, while residue ZN401 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
the force field includes Zn and K parameters. If i seperate them as chain B, then the .gro file is generated, but with a warning
Residue ZN401 has type ‘Ion’, assuming it is not linked into a chain.
Residue K402 has type ‘Ion’, assuming it is not linked into a chain.
Residue K403 has type ‘Ion’, assuming it is not linked into a chain.
My question is since Zn atom have co-ordinate bonds with 3 amino acids, does the warning has any impact on the simulations