Error: Dealing with metal atoms

User discussions
1

GROMACS version:2020.3
GROMACS modification: No
Hello! Everyone,

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
molecule.

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

2

Hi,

I do not exactly understand how you have modified the force field. Thus to that part I can not answer.

An option to deal with ion covalently bonded to residues (without modified the residues database in the force field) is

  1. to build a topology for the protein without ion,
  2. then edit the file protein…itp
  3. add the ion at the end of [ atoms ] (see example)

3246 CC 127 PRO C 3246 0.34 12.011 ; qtot -6.66
3247 OC 127 PRO OT1 3247 -0.67 15.9994 ; qtot -7.33
3248 OC 127 PRO OT2 3248 -0.67 15.9994 ; qtot -8
; add zn in topology
3249 ZN 910 ZN2 ZN 3249 2 65.37

  1. Then add parameter where you need for example in [ bonds ]
    3249 1043 6 0.207 4000 ;
    3249 768 6 0.207 4000 ;

Kind regards
Alessandra

3

Thank you Alessandra, for the procedure. This makes simple and easy to handle metal atoms in proteins. I modified the force field with the parameters specified in https://pubs.acs.org/doi/abs/10.1021/acs.jcim.9b00407.