# Ligand topology

**URL:** <https://gromacs.bioexcel.eu/t/ligand-topology/8716>\
**Category:** User discussions\
**Created:** [March 28, 2024, 5:45am UTC](https://gromacs.bioexcel.eu/t/ligand-topology/8716 "2024-03-28T05:45:54Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Noopur3](https://avatars.discourse-cdn.com/v4/letter/n/b4bc9f/32.png) [@Noopur3](https://gromacs.bioexcel.eu/u/Noopur3)\
**Post date:** [March 28, 2024, 5:45am UTC](https://gromacs.bioexcel.eu/t/ligand-topology/8716/1 "2024-03-28T05:45:54Z")

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GROMACS version: 2021.4  
GROMACS modification: Yes/No  
I am a newbie in molecular dynamics area. I am following Tutorial 5 of the official Gromacs MD Tutorials. I am trying to generate ligand topology file through GGENFF by following the exact method stated in the tutorial only to get high penalty score (186). I am confused how to proceed further. Please guide me.

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**Author:** ![scinikhil](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/scinikhil/32/3483_2.png) [@scinikhil](https://gromacs.bioexcel.eu/u/scinikhil)\
**Post date:** [March 29, 2024, 8:20pm UTC](https://gromacs.bioexcel.eu/t/ligand-topology/8716/2 "2024-03-29T20:20:42Z")

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Please read their webpage FAQ. In general you need to opimise the ligand structure using QM methods and use that optimised geometry for the topology generation. If the penalty is still high you may need to use tools like FFTK to parameterise the molecules.