How to use gmx hbond to analyze hydrogen bond between two chains of a homodimer?

User discussions
1

GROMACS version: 2020.06
GROMACS modification: No
Hello, everyone!
I used gmx hbond command to analyze hydrogen bond between two chains of a homodimer. In index file, the homodimer was splited into chain_A and chain_B by splitch the protein. The I used the following command:
gmx hbond -s md.tpr -f md.xtc -n index.ndx -num A_B.xvg -hbn A_B.ndx -hbm A_B.xpm
The results indicated the hydrogen bonds between Y220 of Chain_A and D192 of Chain_B were generated frequently (>90%). However, when I looked for them using vmd, these hydrogen bonds were handly formed.
Then I made Y220 of Chan_A as a new group, and analyzed the hydrogen bonds between Y220 of Chain_A and Chain_B. The results showed hydrogen bonds were handly formed. I was completely confused.
If someone know the reason, please help me. Thanks!

2

How did you interpret the results to arrive at the conclusion that these two residues formed hydrogen bonds? It seems based on visual follow-up and direct analysis, that was simply an erroneous conclusion.

3

Thank you for your attention and reply.
The results were obtained from the hbond ndx and xpm file. I also used the Hydrogen Bond Matrix analysis from md-davis tools. The results were consistent. I focus on the Y220 site, so I checked the trajectory using vmd. However, hydrogen bonds from Y220 were handly formed.
There was another question. The numbers of the “Hydrogen bonds” were larger than those of “Pairs within 0.35 nm” in the num file, for example:

@ s0 legend “Hydrogen bonds”
@ s1 legend “Pairs within 0.35 nm”
0 23 17
10 23 13
20 18 22
30 19 16
40 18 18
50 17 12
60 20 16