# Generate gromacs topology for hypothetical structure

**URL:** https://gromacs.bioexcel.eu/t/generate-gromacs-topology-for-hypothetical-structure/1894
**Category:** User discussions
**Created:** [April 4, 2021, 11:07am UTC](https://gromacs.bioexcel.eu/t/generate-gromacs-topology-for-hypothetical-structure/1894 "2021-04-04T11:07:31Z")
**Posts on this page:** 1
**Page:** 1

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### Author: ![tuanan](https://avatars.discourse-cdn.com/v4/letter/t/f07891/32.png) [@tuanan](https://gromacs.bioexcel.eu/u/tuanan)
#### Post date: [April 4, 2021, 11:07am UTC](https://gromacs.bioexcel.eu/t/generate-gromacs-topology-for-hypothetical-structure/1894/1 "2021-04-04T11:07:31Z")

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Hi everyone,

I am trying to simulate a hypothetical material based on the graphene layers. However, I am facing some issues trying to generate the ITP file for the material. For the graphene layer, several tools work well, if I consider graphene as a bunch of benzene, but if I do some modifications to the layers I face several problems.

Does anyone know some tool that just recognizes the connections between the atoms? I do not want to find a force field, just create the ITP file with the connections between the atoms.

Thank you.