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

Justin Lemkul jalemkul at vt.edu
Wed May 22 19:15:22 CEST 2019

On 5/22/19 1:04 PM, Neena Susan Eappen wrote:
> 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.

It's a VMD question, so that's the appropriate forum.

You can easily do H-bond analysis in GROMACS with gmx hbond, and it will 
consider all relevant groups. If VMD has some limitation or issue with 
what it defines as H-bond donors or acceptors, again that is their issue.



Justin A. Lemkul, Ph.D.
Assistant Professor
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Virginia Tech Department of Biochemistry
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