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.
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