# Penalty score

**URL:** <https://gromacs.bioexcel.eu/t/penalty-score/1505>\
**Category:** User discussions\
**Created:** [January 28, 2021, 11:31pm UTC](https://gromacs.bioexcel.eu/t/penalty-score/1505 "2021-01-28T23:31:30Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![Amar\_Kumar](https://avatars.discourse-cdn.com/v4/letter/a/ecc23a/32.png) [@Amar\_Kumar](https://gromacs.bioexcel.eu/u/Amar_Kumar)\
**Post date:** [January 28, 2021, 11:31pm UTC](https://gromacs.bioexcel.eu/t/penalty-score/1505/1 "2021-01-28T23:31:30Z")

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GROMACS version:  
GROMACS modification: Yes/No  
Here post your question

I am currently trying to generate the .str file for the small molecule for MD. Using the CGenFF portal I am getting these above cut-off penalties for some. Somehow I minimized the structure using the MMFF94s and then tried again but the penalties remain the same. Then I tried optimizing my molecule by running through gamess and then again tried to get the .str seems like the penalties are worse this time.

I would like to get a general idea of penalties, and why are they getting imposed (higher penalties) on a simple molecule, as what I get from the CGenFF paper it seems as my molecule falls under the two broader categories (simple heterocyclic scaffolds and not some crazy functional groups).

Solution request:  
How to get the penalties under 10? and if I doing so does it affects the integrity of the molecule?

[Ligand\_gamess.log](https://gromacs.bioexcel.eu/uploads/short-url/AnqdcyI34SFlD8G68qx0rD50nVw.log) (8.9 KB) [Ligand\_MMFS94s.log](https://gromacs.bioexcel.eu/uploads/short-url/7K6DJjgpzYLli1AUvvc4ZADgZ6C.log) (6.9 KB)

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**Author:** ![avilla](https://avatars.discourse-cdn.com/v4/letter/a/f1d935/32.png) [@avilla](https://gromacs.bioexcel.eu/u/avilla)\
**Post date:** [January 29, 2021, 10:06am UTC](https://gromacs.bioexcel.eu/t/penalty-score/1505/2 "2021-01-29T10:06:01Z")

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Hi,  
The question is not GROMACS related. Maybe better to contact CGenFF portal developer. Probably they can help you more.  
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:** [January 29, 2021, 1:54pm UTC](https://gromacs.bioexcel.eu/t/penalty-score/1505/3 "2021-01-29T13:54:19Z")

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As I post every week on this forum, the CGenFF publications have the answer here, including tutorials available online that describe how to do parameter refinement. You won’t be able to do much (or any) of that in GROMACS.

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**Author:** ![Amar\_Kumar](https://avatars.discourse-cdn.com/v4/letter/a/ecc23a/32.png) [@Amar\_Kumar](https://gromacs.bioexcel.eu/u/Amar_Kumar)\
**Post date:** [February 1, 2021, 4:30am UTC](https://gromacs.bioexcel.eu/t/penalty-score/1505/4 "2021-02-01T04:30:40Z")

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Thank you.

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**Author:** ![Amar\_Kumar](https://avatars.discourse-cdn.com/v4/letter/a/ecc23a/32.png) [@Amar\_Kumar](https://gromacs.bioexcel.eu/u/Amar_Kumar)\
**Post date:** [February 1, 2021, 4:31am UTC](https://gromacs.bioexcel.eu/t/penalty-score/1505/5 "2021-02-01T04:31:59Z")

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Thank you Dr. Lemkul.