F···H hydrogen bonds

User discussions
1

GROMACS version:
GROMACS modification: Yes/No
Hello gmx users,

I have a polymer [Poly] and ligand [LigF] system and I have genrated the .gro, .xtc and .ndx files. They have -OH and -F groups. I want to calculate the number of O···H, F···H and total hydrogen bonds between the Poly and LigF.

  1. How to use gmx hbond in such case? I saw O and N atoms are acceptor in the hbond tool. I am looking for idea to include F-atom as acceptor in the computation. How can I count the F···H hydrogen bonds?

Please give suggestion for a way out here.
Thank you in advance.

Regards
ranajit

2

gmx hbond operates based solely on atom name, so the only way to make this work is to change the names of your F atoms to, e.g. O and recompile a .tpr file to be used for this particular analysis.

3

Hello @jalemkul ,

Thank you for the quick response and suggestion.
Can you please write in more detail? I do not understand.

At this moment, I can only change the .gro file at t0 as,
“”"
17T4H H5 2162 5.348 5.115 7.277
18A12 F1 2163 5.205 4.662 4.209
18A12 C16 2164 5.078 4.623 4.191
18A12 F2 2165 5.068 4.518 4.277
18A12 F3 2166 5.070 4.577 4.067
18A12 C15 2167 4.976 4.735 4.219
“”"
to
“”"
17T4H H5 2162 5.348 5.115 7.277
18A12 OF1 2163 5.205 4.662 4.209
18A12 C16 2164 5.078 4.623 4.191
18A12 OF2 2165 5.068 4.518 4.277
18A12 OF3 2166 5.070 4.577 4.067
18A12 C15 2167 4.976 4.735 4.219
“”"
Is it a correct way?
How to change or recompile .tpr file? what about the trajectory (.xtc file), how to change it?

Regards
Ranait

4

Change the coordinate and topology files to avoid grompp warnings when generating the new .tpr file. You don’t need to touch the .xtc file; it has no topological information, just coordinates and box information.

5

Hello @jalemkul ,

Thank you very much for the help and suggetions. It worked fine.

I got results like,
“”"
@ s1 legend “Pairs within 0.35 nm”
0 0 2
0.2 0 1
0.4 0 2
0.6 0 2
0.8 0 1
1 0 2
1.2 0 1
1.4 0 2
1.6 0 2
1.8 1 1
2 0 1
“”"
I guess the 1st and 3rd columns are time and No. of H-bonds.
What is in the 2nd column of the result? If you comment on it will be beneficial.

Regards
Ranajit

6

Plot the file and you will see :)

Time, H-bonds, Pairs within 0.35 that do not satisfy the angle criterion to be an H-bond

7

Thank you for the detailed information.

Is there any document where I can find the details of distance and angle cutoffs and why they are made in such way. I am curious to read more about it.

Regards
Ranajit

8

The 0.35-nm distance cutoff comes from the O-O RDF peak in pure water, IIRC. The angle criterion varies a bit by software package but the value is conventionally accepted. If anyone can point to an actual literature reference, that would be great, but I don’t know it.