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 A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129


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