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

Neena Susan Eappen neena.susaneappen at mail.utoronto.ca
Wed May 22 19:04:39 CEST 2019

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,

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

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