[gmx-users] H-Bond from peptide capping group

[Neena Susan Eappen]

Hello gromacs users,

I uploaded a peptide structure on VMD with its trajectory (using gromacs package) and used H-bond plugin to figure out possible H bonds. The C-terminus has a capping amide group. The H-bond plugin never catches any H-bond information from that capping group. My guess is the capping group is considered as a separate entity (not part of the peptide). Any insight would be appreciated.

Thank you,
Neena

P.S. I received no answer to this question on VMD mailing list, hence asking here.