# Terminal methyl atoms not connected after pdb2gmx

**URL:** <https://gromacs.bioexcel.eu/t/terminal-methyl-atoms-not-connected-after-pdb2gmx/8374>\
**Category:** User discussions\
**Created:** [February 19, 2024, 3:20pm UTC](https://gromacs.bioexcel.eu/t/terminal-methyl-atoms-not-connected-after-pdb2gmx/8374 "2024-02-19T15:20:43Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![reaham](https://avatars.discourse-cdn.com/v4/letter/r/d6d6ee/32.png) [@reaham](https://gromacs.bioexcel.eu/u/reaham)\
**Post date:** [February 19, 2024, 3:20pm UTC](https://gromacs.bioexcel.eu/t/terminal-methyl-atoms-not-connected-after-pdb2gmx/8374/1 "2024-02-19T15:20:43Z")

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GROMACS version: 2020.1-Ubuntu-2020.1-1  
GROMACS modification: No  
Here post your question  
Error message  
In moleculetype ‘Protein\_chain\_A22’ 3 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.

Atom 46 ‘H16A’ in moleculetype ‘Protein\_chain\_B22’ is not bound by a potential or constraint to any other atom in the same moleculetype.

Atom 47 ‘H16B’ in moleculetype ‘Protein\_chain\_B22’ is not bound by a potential or constraint to any other atom in the same moleculetype.

Atom 48 ‘H16C’ in moleculetype ‘Protein\_chain\_B22’ is not bound by a potential or constraint to any other atom in the same moleculetype.

These (lipid chain terminal methyl) atoms are bound to the corresponding carbon in the starting pdb file.  
Somehow pdb2gmx messes up the connectivity. Manually adding the relevant bonds to the itp files leads to errors when running grompp NVT simulations.  
Any ideas?

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**Author:** ![milosz.wieczor](https://avatars.discourse-cdn.com/v4/letter/m/b19c9b/32.png) [@milosz.wieczor](https://gromacs.bioexcel.eu/u/milosz.wieczor)\
**Post date:** [February 20, 2024, 2:22pm UTC](https://gromacs.bioexcel.eu/t/terminal-methyl-atoms-not-connected-after-pdb2gmx/8374/2 "2024-02-20T14:22:14Z")

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Did you create it through a custom .rtp entry? If so, make sure the `[bonds]` section included bonds to `H16[ABC]`.

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**Author:** ![reaham](https://avatars.discourse-cdn.com/v4/letter/r/d6d6ee/32.png) [@reaham](https://gromacs.bioexcel.eu/u/reaham)\
**Post date:** [February 21, 2024, 8:50am UTC](https://gromacs.bioexcel.eu/t/terminal-methyl-atoms-not-connected-after-pdb2gmx/8374/3 "2024-02-21T08:50:59Z")

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Hi Milosz

Thanks - that was it!

Ian