[gmx-users] Analyzing Hydrogen Bonding Interactions using Gromacs

[Chenyu Liu]

Hi gromacs users,

I was trying to analyze hydrogen bonding interaction of a protein and
intended to obtain the detailed list of interactions. Such as amine
hydrogen from Lys A residue forms a hydrogen bond with the backbone
carbonyl oxygen of some other residue. I tried the gmx hbond command but I
cannot find one option for this purpose. I could get results such as hbond
donor numbers, distance distribution, but not detailed information about
the interactions. I was wondering if there is any command to derive this
information from the trajectory. Also, if I wanted to analyze hydrogen bond
formed by a specific type of donor/acceptor (such as side chain hydrogen as
a donor), what should I do to specify that?

I have tried using vmd software (there is a hbond analysis in the
extension) to analyze the trajectory, and it worked pretty well for shorter
trajectories. My trajectory consists of 5000 frames and when I loaded the
trajectory the program terminates at around 4000 frames. So, I think I
should divide the trajectories into smaller pieces and analyze each piece.
My question is that is there a way I can write a bash script to automate
the process so that I can analyze these shorter trajectories without
loading them by hand (otherwise there will be 100 shorter trajectories,
since I have run several parallel long trajectories). I can write bash
script for all operations involving gromacs, but not vmd.

I would really appreciate it if you could answer my question, or point out
some resources which I could refer to. Thanks in advance!

Best regards,
Chenyu