# Inter chain hydrogen bond calculation

**URL:** <https://gromacs.bioexcel.eu/t/inter-chain-hydrogen-bond-calculation/11056>\
**Category:** User discussions\
**Created:** [January 16, 2025, 5:51pm UTC](https://gromacs.bioexcel.eu/t/inter-chain-hydrogen-bond-calculation/11056 "2025-01-16T17:51:33Z")\
**Posts on this page:** 3\
**Page:** 1

<div class="post-metadata">

**Author:** ![com\_gro](https://avatars.discourse-cdn.com/v4/letter/c/f475e1/32.png) [@com\_gro](https://gromacs.bioexcel.eu/u/com_gro)\
**Post date:** [January 16, 2025, 5:51pm UTC](https://gromacs.bioexcel.eu/t/inter-chain-hydrogen-bond-calculation/11056/1 "2025-01-16T17:51:33Z")

</div>

Hello everyone,  
I need your help to calculate inter-chain hydrogen bonds.  
I have three chains: A, B, and C. Their respective indices are as follows:

```auto
$comm make_ndx -f "$TPR_FILE" -o "$index_FILE"<< EOF
a 1-860
name 17 chain_a
a 861-1720 
name 18 chain_b
a 1721-2580 
name 19 chain_c
18 | 19
name 20 chain_bc
17 | 19
name 21 chain_ac
17 | 18
name 22 chain_ab

```

I am using the following code to generate the results.  
Here, as for example, when chain\_a (17) is a donar then chain\_bc (20) is acceptor.Same for the others.

```auto
chains=("chaina" "chainb" "chainc")

# Iterate over each chain
for chain in "${chains[@]}"; do
    GRO_FILE="${BASE_PATH}/trimer_traj5_npt_55.tpr"
    XTC_FILE="${BASE_PATH}/trimer_traj5_55.xtc"
    index_file="${BASE_PATH}/analysis/hbond/index.ndx"
    hb_FILE="${BASE_PATH}/analysis/hbond/1_hbonds_${chain}.xvg"
    o_FILE="${BASE_PATH}analysis/hbond/hbond_${chain}.ndx"
    
    # Run GROMACS hbond command
    if ["$chain" = "chaina"]; then
        (echo 17; echo 20) | $comm hbond -f "$XTC_FILE" -s "$GRO_FILE" -n "$index_file" -num "$hb_FILE" -cutoff 0.35 -m 
    elif ["$chain" = "chainb"]; then
        (echo 18; echo 21) | $comm hbond -f "$XTC_FILE" -s "$GRO_FILE" -n "$index_file" -num "$hb_FILE" -cutoff 0.35 -m 
    elif ["$chain" = "chainc"]; then
        (echo 19; echo 22) | $comm hbond -f "$XTC_FILE" -s "$GRO_FILE" -n "$index_file" -num "$hb_FILE" -cutoff 0.35 -m 
    fi
done

```

However, when I add all three files together, it generates a higher number of hydrogen bonds than expected.  
Could you please tell me the right way to calculate inter-chain hbond?  
Thanks in advance!

---

<div class="post-metadata">

**Author:** ![cathrine](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/cathrine/32/1736_2.png) [@cathrine](https://gromacs.bioexcel.eu/u/cathrine)\
**Post date:** [January 17, 2025, 3:35pm UTC](https://gromacs.bioexcel.eu/t/inter-chain-hydrogen-bond-calculation/11056/2 "2025-01-17T15:35:45Z")

</div>

Hi!

How many selections do you have in your index file? If you have three chains you should have three selections, one for each chain. You can of course define the chains manually with indices like you have done, but it’s probably easier (and safer) to use “splitch 1” to get the three protein chains (1 should represent the protein). Then, you can just pass this index file to gmx hbond, select the two chains between which you want to calculate the number of hbonds and then add the results together. Note that you can also use gmx select to create the index file, but splitch in make\_ndx is probably the easiest option.

Let me know if this helped!

---

<div class="post-metadata">

**Author:** ![com\_gro](https://avatars.discourse-cdn.com/v4/letter/c/f475e1/32.png) [@com\_gro](https://gromacs.bioexcel.eu/u/com_gro)\
**Post date:** [January 17, 2025, 4:22pm UTC](https://gromacs.bioexcel.eu/t/inter-chain-hydrogen-bond-calculation/11056/4 "2025-01-17T16:22:09Z")

</div>

Hello Cathrine,  
Thank you so much. It works!

Below is my bash script:

```auto
BASE_PATH="/home/md_simulation"
comm=gmx

$comm make_ndx -f "$TPR_FILE" -o "$index_FILE"<< EOF
a 1-860
name 17 chain_a
a 861-1720 
name 18 chain_b
a 1721-2580 
name 19 chain_c
q
EOF
chains=("chaina" "chainb" "chainc")

# Create the analysis directory if it doesn't exist
mkdir -p "${BASE_PATH}"

# Iterate over each chain
for chain in "${chains[@]}"; do
    GRO_FILE="${BASE_PATH}/trimer_traj5_npt_55.tpr"
    XTC_FILE="${BASE_PATH}/trimer_traj5_55.xtc"
    index_file="${BASE_PATH}/analysis/hbond/index.ndx"
    hb_FILE="${BASE_PATH}/analysis/hbond/1_hbonds_${chain}.xvg"
    o_FILE="${BASE_PATH}/analysis/hbond/hbond_${chain}.ndx"
    
    # Run GROMACS hbond command
    if ["$chain" = "chaina"]; then
        $comm hbond -f "$XTC_FILE" -s "$GRO_FILE" -r chain_a -t chain_b -n "$index_file" -num "$hb_FILE" -cutoff 0.35 -m -o "$o_FILE"
    elif ["$chain" = "chainb"]; then
        $comm hbond -f "$XTC_FILE" -s "$GRO_FILE" -r chain_b -t chain_c -n "$index_file" -num "$hb_FILE" -cutoff 0.35 -m -o "$o_FILE"
    elif ["$chain" = "chainc"]; then
        $comm hbond -f "$XTC_FILE" -s "$GRO_FILE" -r chain_c -t chain_a -n "$index_file" -num "$hb_FILE" -cutoff 0.35 -m -o "$o_FILE"
    fi
done
```