# Using gmx hbond to analyse hbonds % occupancy.

**URL:** <https://gromacs.bioexcel.eu/t/using-gmx-hbond-to-analyse-hbonds-occupancy/107>\
**Category:** User discussions\
**Created:** [May 11, 2020, 3:57am UTC](https://gromacs.bioexcel.eu/t/using-gmx-hbond-to-analyse-hbonds-occupancy/107 "2020-05-11T03:57:17Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![skamairese](https://avatars.discourse-cdn.com/v4/letter/s/8e7dd6/32.png) [@skamairese](https://gromacs.bioexcel.eu/u/skamairese)\
**Post date:** [May 11, 2020, 3:57am UTC](https://gromacs.bioexcel.eu/t/using-gmx-hbond-to-analyse-hbonds-occupancy/107/1 "2020-05-11T03:57:17Z")

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Hello,

How do I use gmx hbond to find hbonds % occupancy?  
I am doing H-bond analyses, and I want to get % h-bond occupancy between a protein and a peptide. I am using the gmx hbond, and I created indices for the protein and for the peptide to analyze hbonds between the two indices. However, none of the output has the donor-acceptor % occupancy.

Any suggestions will be appreciated.

Thank you,  
Seraphine.

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**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\
**Post date:** [May 11, 2020, 9:06am UTC](https://gromacs.bioexcel.eu/t/using-gmx-hbond-to-analyse-hbonds-occupancy/107/2 "2020-05-11T09:06:27Z")

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Hi,  
You can not get % occupancy directly from gmx hbond. You can extract the occupancy by analysing the time series of each selected hydrogen bond. To get information you need, the option -hbn -hbm ( gmx hbond) may be useful.  
Best regards  
Alessandra

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**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [May 12, 2020, 12:51pm UTC](https://gromacs.bioexcel.eu/t/using-gmx-hbond-to-analyse-hbonds-occupancy/107/3 "2020-05-12T12:51:59Z")

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I have a script that does this: [https://osf.io/3wunt/](https://osf.io/3wunt/)

Please make sure to read the instructions in the header carefully; it is a clunky script that I wrote many years ago so it requires some changes to the input files to make everything work.