[gmx-users] [gmx users] Terminal amide hydrogens not included in H-bond analysis

[Sahil Lall]

Hello, 

Though I don't know the answer to your question, I can offer a
workaround for the task. I have simulated such C-terminally amidated
peptides in vacuum before and I performed the same analysis using the
Hydrogen bonds plugin in VMD. 

Hope this helps. 

Cheers, 

Sahil 

On 2020-04-28 07:20, 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?
> 
> Many thanks,
> Neena