[gmx-users] Analyzing Hydrogen Bonding Interactions using Gromacs

[Chenyu Liu]

This is what I mean by detailed information:
........vi hbonds-details.dat
 Found 360 hbonds.
donor        acceptor    occupancy
LYS21-Side-NZ    GLU24-Side-OE2      17.31%
VAL15-Main-N     GLU17-Side-OE1      40.38%
LYS16-Main-N     GLU17-Side-OE1      11.54%
 ARG190-Side-NH2      ASP161-Side-OD2     61.54%
LYS23-Main-N     LEU19-Main-O    19.23%
ASP25-Main-N     LYS21-Main-O    21.15%
SER159-Side-OG   TYR156-Main-O   30.77%

this .dat file is generated by vmd's hydrogen bond analysis extension.

I hope this would clarify the question I have.



On Thu, Feb 27, 2020 at 1:42 PM Chenyu Liu <liu00554 at umn.edu> wrote:

> 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
>
>