[gmx-users] [gmx users] Terminal amide hydrogens not included in H-bond analysis

[Justin Lemkul]

On 4/27/20 9:50 PM, Neena Susan Eappen wrote:
> Hello gromacs users,
>
> My peptide has an amide group at the C-terminus. Hydrogen bond analysis using gmx hbond does not take into account H-bond donors (NH2) from the amide group (Note: this NH2 is considered as a residue according to opls ff). What might be happening here?

How do you know this group isn't being factored into the analysis? The 
NH2 residue is recognized as a protein residue by default and the 
analysis should consider all N-H pairs as H-bond donors.

-Justin

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Justin A. Lemkul, Ph.D.
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