You can use VMD

Dear Urszula, 

it would be probably much easier if you tell us what do you need/expect. Vikash has right that VMD may be really usable, but it's not so comfortable to use in some cases (like massive number of simulations/frames, some specific parameters etc.).

Specify your needs and I'll try to give you a hint :)

I don't think g_bond is the correct tool, because it measures only distances and most hydrogen bonding criteria take both distances and angles into account.  

Did you mean g_hbond?  I believe that should contain the output you need, if you look at the help text and provide the correct output file names.  (-hbm: existence matrix for all hydrogen bonds over all frames)

How about trying the MDTraj tool? (http://mdtraj.org/latest/) It is free, fast, and implements the analysis you want. There are two hydrogen bonding criteria available:

See http://mdtraj.org/latest/api/generated/mdtraj.baker_hubbard.html and http://mdtraj.org/latest/api/generated/mdtraj.wernet_nilsson.html

To use it, you would write a Python script like this:

import mdtraj as md

t = md.load('trajectory.xtc', top='trajectory.pdb')

md.wernet_nilsson(traj)

This would give you a list of hydrogen bonds that satisfy the criterion for each frame, which you could then use to compute the occupancy.

The baker_hubbard function behaves differently and requires you to specify an occupancy as the input; it returns just a single set of hydrogen bonds that meet this occupancy threshold for the whole trajectory.  You could run this using several occupancies and build a histogram this way.

I have just installed MDtraj, but I am not able to find any informations how to run it?

Here are examples for how to run it:

http://mdtraj.org/latest/examples/index.html

Did you try to use it for a huge trajectory file? I would like to run hbond analysis on a 60 ns trajectory or at least 20ns. I went through exmaples but still having the memory error… :(

MDTraj is routinely used to process very large trajectories (> 50,000 atoms for microseconds). 

How often are you sampling your data?  Are you keeping the water?

You might be able to preprocess your trajectory by stripping the water away, or subsample at a lower time resolution.  Also feel free to discuss your issue on the forums. :)

http://discourse.mdtraj.org/

60ns doesn't mean file is huge - how many atoms? Or better - gigs?

You can try to use lower density frames (every 5th or 10th) - it should still be representative.

VMD is still - probably - one of the most comfortable tools, but if you can convert your trajectory to dcd format - you can try to use EUCB (pretty nice, it allows to analyse big files).

You can visualize your obtained structure in pymol and try this command 

list_hbonds.py

Hi.

You may want to try HBonanza --very useful to view Hbond occupancy. It works for intra-hydrogen bonding within protein, but not sure if it can be used for inter-hydrogen bonding. Trying won't hurt, thou :)

It uses multiple pdbs as the input. Just convert the .xtc to a compiled pdbs. 

http://nbcr.ucsd.edu/data/sw/hosted/hbonanza/

Hi.

I also have some problem in learning how to use MDTraj and HBonanza. It is difficult for beginners like me. Fortunately, I've found a useful python script name readHBmap.py . Its a script that can read hydrogen bond from hydrogen bond maps file (.xpm) generated by g_hbond . It gave an output list of donors-acceptor pair with percentage of occupancy . You can obtain the script from here http://www.gromacs.org/Downloads/User_contributions/Other_software . (Find readHBmap.tar.gz from the list)

Hope it helps ... ^^,

Thank you I will have a look at it. You are right its not that easy to run mdtraj or bonanza. After mdtraj installation I am still not getting exactly what I would like to have regarding the H-bond analysis. 

I  run the readHBmap.py script but typing: ./readHBmap.py -hbm hbmap.xpm -hbn hbond.ndx -f ../../md6.gro -o occupancy.xvg -op pairs.dat -t 1

and I received:

-> Results for readHBmap.py (Author: Ricardo O. S Soares)

--> Found 8 valid hydrogen bond pairs with occupancy of more than 1.0%

--> The hydrogen bond map (hbmap.xpm) has 1201 frames

Pair ID | donor-acceptor | Atom Number | Occupancy (%) | Pair ID

1 ( ) - ( ) - 13.1 1

2 ( ) - ( ) - 3.1 2

3 ( ) - ( ) - 28.0 3

4 ( ) - ( ) - 3.7 4

5 ( ) - ( ) - 7.8 5

6 ( ) - ( ) - 3.8 6

7 ( ) - ( ) - 19.6 7

I was wondering what did may go wrong here?