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

**URL:** <https://gromacs.bioexcel.eu/t/atoms-are-not-bound-by-a-potential-or-constraint-to-any-other-atom-in-the-same-moleculetype/3510>\
**Category:** User discussions\
**Created:** [January 20, 2022, 5:24pm UTC](https://gromacs.bioexcel.eu/t/atoms-are-not-bound-by-a-potential-or-constraint-to-any-other-atom-in-the-same-moleculetype/3510 "2022-01-20T17:24:01Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![lanselibai](https://avatars.discourse-cdn.com/v4/letter/l/e9c0ed/32.png) [@lanselibai](https://gromacs.bioexcel.eu/u/lanselibai)\
**Post date:** [January 20, 2022, 5:24pm UTC](https://gromacs.bioexcel.eu/t/atoms-are-not-bound-by-a-potential-or-constraint-to-any-other-atom-in-the-same-moleculetype/3510/1 "2022-01-20T17:24:01Z")

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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

```auto
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?

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**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [January 21, 2022, 4:09am UTC](https://gromacs.bioexcel.eu/t/atoms-are-not-bound-by-a-potential-or-constraint-to-any-other-atom-in-the-same-moleculetype/3510/2 "2022-01-21T04:09:21Z")

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> [@lanselibai](#):
>
> Do I need to worry about this?

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.

> [@lanselibai](#):
>
> If so, how can I add a bond/potential/constraint to the zinc ion?

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

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<div class="post-metadata">

**Author:** ![lanselibai](https://avatars.discourse-cdn.com/v4/letter/l/e9c0ed/32.png) [@lanselibai](https://gromacs.bioexcel.eu/u/lanselibai)\
**Post date:** [January 21, 2022, 4:22pm UTC](https://gromacs.bioexcel.eu/t/atoms-are-not-bound-by-a-potential-or-constraint-to-any-other-atom-in-the-same-moleculetype/3510/3 "2022-01-21T16:22:14Z")

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

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<div class="post-metadata">

**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [January 22, 2022, 3:36am UTC](https://gromacs.bioexcel.eu/t/atoms-are-not-bound-by-a-potential-or-constraint-to-any-other-atom-in-the-same-moleculetype/3510/4 "2022-01-22T03:36:10Z")

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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.

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**Author:** ![lanselibai](https://avatars.discourse-cdn.com/v4/letter/l/e9c0ed/32.png) [@lanselibai](https://gromacs.bioexcel.eu/u/lanselibai)\
**Post date:** [January 23, 2022, 9:05pm UTC](https://gromacs.bioexcel.eu/t/atoms-are-not-bound-by-a-potential-or-constraint-to-any-other-atom-in-the-same-moleculetype/3510/5 "2022-01-23T21:05:25Z")

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