I have simulated a protein-protein complex in GROMACS. During Hydrogen bond analysis for individual residues using gmx hbond, I am getting results as H-bond average 1.012 for 2134 frames. What to infer from the results?
It means that the proteins are weakly bounded by H-bonds (only one h-bond for two proteins). However, this does not mean they are not strongly interaction or not. Before the run, you could use energy groups and define two separate groups for each proteins and then you could get some information about LJ and electrostatic interactions between the proteins.
A more sophisticated way would be performing PMF.
It is not clear from the description that, between which two molecules/residues you want to study the H-bond dynamics. how you are choosing the angle and distance cut-offs?
Sometimes visualising helps.
It is not clear from your description what kind of system we are dealing with, so we cannot give you complete responses.
An average 1.012 hydrogen bonds may SEEM rather low, but if your interface is mostly hydrophobic residues and the your contacts are predominantly the side-chains, or if you are dealing with only three residues when analyzing the contact site... or since you only have 2134 frames of what I assume are 2 ps each... (need details, need details, need details).
The point is that without more information it is impossible to say if what you see is appropriate (thus conclusions are hard to infer).
Please explain your system, and aim to describe it with EXCRUCIATING detail. Then we can advise you more appropriately.
Can you tell me how do you specify individual residues for this analysis?
The basic way to do that is to define different groups in an index.ndx file.
In most of my runs I am looking for one particular interaction, so I only declare individual donors or acceptors:
For example, assuming I have only these two entries in the index file:
[N-H]
100 101
[O]
200
> index.ndx
The numbers correspond to the numbering in the .gro (and thus .tpr) file(s). You can make one of these 'residues' as large as you want and the calculator determines all hydrogen bonds between all members of each 'residue' with the following command.
echo 0 1 | gmx hbond -s top.tpr -f traj.xtc -n index.ndx -num hbond.xvg
The result comes out as an ASCII-type list of all the hydrogen-bonds between the particular residues over the entire trajectory - in this case between the one N-H group and one O group you selected, so it should generally be only one H-bond at a time.
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