# Software to parametrize small molecule

**URL:** <https://gromacs.bioexcel.eu/t/software-to-parametrize-small-molecule/9408>\
**Category:** User discussions\
**Created:** [June 17, 2024, 3:12am UTC](https://gromacs.bioexcel.eu/t/software-to-parametrize-small-molecule/9408 "2024-06-17T03:12:12Z")\
**Posts on this page:** 2\
**Page:** 1

<div class="post-metadata">

**Author:** ![DrOneLeg](https://avatars.discourse-cdn.com/v4/letter/d/eb8c5e/32.png) [@DrOneLeg](https://gromacs.bioexcel.eu/u/DrOneLeg)\
**Post date:** [June 17, 2024, 3:12am UTC](https://gromacs.bioexcel.eu/t/software-to-parametrize-small-molecule/9408/1 "2024-06-17T03:12:12Z")

</div>

GROMACS version:2021.6  
GROMACS modification: No  
Hi, long time listener first time caller

I’m currently looking for a way to parametrize small molecules (preferably in a charmm force field though that’s not a deal breaker) based on an .mol2,.pdb,.sdf etc input in order too simulate them with a protein.

While I’m aware of some websites that would allow me to do this due to restrictions being placed upon me I’m only going to be able to use software that can be run locally on my machine.  
I’ve attempted to find some software that would work though have yet to find anything satisfactory.

Any recommendations would be greatly appreciated.  
Thanks in advance.

---

<div class="post-metadata">

**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\
**Post date:** [June 17, 2024, 10:58am UTC](https://gromacs.bioexcel.eu/t/software-to-parametrize-small-molecule/9408/2 "2024-06-17T10:58:08Z")

</div>

Have a look at [GROMACS / STaGE · GitLab](https://gitlab.com/gromacs/stage). It can generate Charmm compatible topologies/parameters. It needs MATCH and openbabel for that. It can also generate parameters for other force fields, but then needs ACPYPE and Antechamber.