# High Penalty Score in CGENFF topology

**URL:** <https://gromacs.bioexcel.eu/t/high-penalty-score-in-cgenff-topology/10821>\
**Category:** User discussions\
**Tags:** topology\
**Created:** [December 15, 2024, 4:19pm UTC](https://gromacs.bioexcel.eu/t/high-penalty-score-in-cgenff-topology/10821 "2024-12-15T16:19:30Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![onuratesss98](https://avatars.discourse-cdn.com/v4/letter/o/8e8cbc/32.png) [@onuratesss98](https://gromacs.bioexcel.eu/u/onuratesss98)\
**Post date:** [December 15, 2024, 4:19pm UTC](https://gromacs.bioexcel.eu/t/high-penalty-score-in-cgenff-topology/10821/1 "2024-12-15T16:19:30Z")

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GROMACS version:2021.4  
GROMACS modification: No

Hi, I’m currently learning how to do MD analysis by myself and after following the instructions on the Gromacs tutorial page, I wanted to do a MD analysis by myself but the ligand, Omipalisib, gives me high penalty score when I form topology file in the system.

| **Uploaded Mol2** | : unk\_fix.mol2 |
| --- | --- |
| **Job Name** | : unk\_fix |
| **Options Selected** | : |

- Output Mol2
- Include Warnings
- Include Debug Info

| **Param Penalty** | : 213.500 |
| --- | --- |
| **Charge Penalty** | : 76.732 |

The FFParam program can be used to facilitate the optimization of parameters for molecules with high “Param” and/or “Charge” penalties. Visit [FFParam](https://ffparam.silcsbio.com/) to learn more.

I’m also new into bioinformatics so please can you explain it to me what I should do with step by step. Thank you.