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

[Neena Susan Eappen]

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?

Many thanks,
Neena