# .str files

**URL:** <https://gromacs.bioexcel.eu/t/str-files/1379>\
**Category:** User discussions\
**Created:** [January 4, 2021, 9:15pm UTC](https://gromacs.bioexcel.eu/t/str-files/1379 "2021-01-04T21:15:31Z")\
**Posts on this page:** 2\
**Page:** 1

<div class="post-metadata">

**Author:** ![konstantina](https://avatars.discourse-cdn.com/v4/letter/k/278dde/32.png) [@konstantina](https://gromacs.bioexcel.eu/u/konstantina)\
**Post date:** [January 4, 2021, 9:15pm UTC](https://gromacs.bioexcel.eu/t/str-files/1379/1 "2021-01-04T21:15:31Z")

</div>

GROMACS version: 2018.1  
GROMACS modification: Yes/No  
Here post your question  
I have generated the .str file for a small organic compound, using the CHARMM General Force Field server. However, I am getting a high number of penalties in the produced. I have previously optimized the geometry of my structure using Avogadro, but that doesn’t seem to work. I realize that this is not a problem of GROMACS, but I do need a solution. I have also downloaded the FFParam GUI server, but I cannot understand if I am doing the procedure the correct way. Thank you in advance.

---

<div class="post-metadata">

**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 5, 2021, 3:51pm UTC](https://gromacs.bioexcel.eu/t/str-files/1379/2 "2021-01-05T15:51:54Z")

</div>

FFParam has tutorials and the CGenFF paper from 2010 is itself a case study in how to parametrize a molecule. Parametrization with the CHARMM or CGenFF force field requires a combination of QM and MM calculations, for which GROMACS is not particularly well suited.