On 5/5/20 12:12 PM, Neena Susan Eappen wrote:
Thank you Sahil, I will try VMD plugin for H-bond analysis.
Thank you Justin for your reply, it looks like gmx hbond considers only one N-H
as donor when part of NH2 group. Please take a look at this file.
This is what gmx hbond does by default,
Thank you Sahil, I will try VMD plugin for H-bond analysis.
Thank you Justin for your reply, it looks like gmx hbond considers only one N-H
as donor when part of NH2 group. Please take a look at this file.
https://drive.google.com/file/d/1EgJPbHXNCo--VFOoy1YYolBx3XKBKpiH/view?usp=sharing
Many tha
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). Wh
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
