Atoms are not bound by a potential or constraint to any other atom in the same moleculetype

User discussions
1

GROMACS version:2021
GROMACS modification: No
Here post your question

I have a zinc atom in the PDB file, which is successfully recognised as +2 charge during pdb2gmx, and merged with the protein as the same moleculetype.

During the ionisation step
gmx grompp -f ions.mdp -c protein_solv.gro -p topol.top -o ions.tpr -v -maxwarn 1

it says

Atom 16085 'ZN' in moleculetype 'Protein_chain_L' is not bound by a potential or constraint to any other atom in the same moleculetype.

NOTE 3 [file topol.top, line 151665]:
In moleculetype 'Protein_chain_L' 1 atoms are not bound by a potential or
  constraint to any other atom in the same moleculetype. Although
  technically this might not cause issues in a simulation, this often means
  that the user forgot to add a bond/potential/constraint or put multiple
  molecules in the same moleculetype definition by mistake. Run with -v to
  get information for each atom.

Do I need to worry about this? If so, how can I add a bond/potential/constraint to the zinc ion?

2

It depends on whether the force field model you’ve chosen can maintain appropriate Zn2+ coordination relying solely on nonbonded interactions. This is not often the case with simple additive, monoatomic representations of these species.

You’ll have to manually add anything like this into the topology if you think it is necessary.

3

Hi Justin, thank you. I use amber14sb forcefield. Could you please explain the meaning of “simple additive, monoatomic representations”?

4

Transition elements are notoriously hard to model and various approaches have been employed. The term “additive” means nonpolarizable. “Monoatomic” means there is one particle representing the ion, whereas other groups have derived multi-site models in which charge is delocalized over them to mimic orbital effects. You will need to determine, based on examination of prior literature, whether or not you need a different model or to assign some kind of bonded connections between the ion and its ligating residues.

1 Like
5

Thank you Justin, it seems to be quite difficult to model. I will look into literature.