# System optimization

**URL:** <https://gromacs.bioexcel.eu/t/system-optimization/5121>\
**Category:** User discussions\
**Created:** [October 27, 2022, 6:07pm UTC](https://gromacs.bioexcel.eu/t/system-optimization/5121 "2022-10-27T18:07:47Z")\
**Posts on this page:** 9\
**Page:** 1

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**Author:** ![vadiambos](https://avatars.discourse-cdn.com/v4/letter/v/0ea827/32.png) [@vadiambos](https://gromacs.bioexcel.eu/u/vadiambos)\
**Post date:** [October 27, 2022, 6:07pm UTC](https://gromacs.bioexcel.eu/t/system-optimization/5121/1 "2022-10-27T18:07:47Z")

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GROMACS version: 2020.1-Ubuntu-2020.1-1  
GROMACS modification: No  
Hi everyone!  
I have some problem with system optimization.  
I have a task to trace the molecular dynamics of berberine in water. To do this, I need to put berberine molecules in a water box. There was a problem described in the screenshot.  
Used the command: gmx pdb2gmx -f \*\*\* -o \*\*\* -water spce

 ![problem](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/4/44aaacd5daba8b3c7fc7ada108e8c5b4a3305801.jpeg)

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**Author:** ![vadiambos](https://avatars.discourse-cdn.com/v4/letter/v/0ea827/32.png) [@vadiambos](https://gromacs.bioexcel.eu/u/vadiambos)\
**Post date:** [October 27, 2022, 6:09pm UTC](https://gromacs.bioexcel.eu/t/system-optimization/5121/2 "2022-10-27T18:09:56Z")

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I know that GROMACS have a force fields for proteins. Is there an option to add a force field for non-protein structures?

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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:** [October 27, 2022, 6:37pm UTC](https://gromacs.bioexcel.eu/t/system-optimization/5121/3 "2022-10-27T18:37:21Z")

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There is no force field that will automatically parametrize any arbitrary species. You have to parametrize this molecule and provide a residue definition for it (`.rtp` entry) or use non-GROMACS tools to produce its topology.

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<div class="post-metadata">

**Author:** ![vadiambos](https://avatars.discourse-cdn.com/v4/letter/v/0ea827/32.png) [@vadiambos](https://gromacs.bioexcel.eu/u/vadiambos)\
**Post date:** [October 27, 2022, 6:53pm UTC](https://gromacs.bioexcel.eu/t/system-optimization/5121/4 "2022-10-27T18:53:18Z")

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Thanks a lot.  
What a program i can use to get a .top file?

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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:** [October 27, 2022, 7:12pm UTC](https://gromacs.bioexcel.eu/t/system-optimization/5121/5 "2022-10-27T19:12:07Z")

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There’s one for every force field - CGenFF for CHARMM, Antechamber/AcPype for AMBER, LigParGen for OPLS, ATB for GROMOS, etc.

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<div class="post-metadata">

**Author:** ![vadiambos](https://avatars.discourse-cdn.com/v4/letter/v/0ea827/32.png) [@vadiambos](https://gromacs.bioexcel.eu/u/vadiambos)\
**Post date:** [October 27, 2022, 7:30pm UTC](https://gromacs.bioexcel.eu/t/system-optimization/5121/6 "2022-10-27T19:30:39Z")

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Thanks.  
I will try to do something with this.

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<div class="post-metadata">

**Author:** ![vadiambos](https://avatars.discourse-cdn.com/v4/letter/v/0ea827/32.png) [@vadiambos](https://gromacs.bioexcel.eu/u/vadiambos)\
**Post date:** [October 27, 2022, 7:41pm UTC](https://gromacs.bioexcel.eu/t/system-optimization/5121/7 "2022-10-27T19:41:00Z")

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> [@jalemkul](#):
>
> LigParGen

Forgot to ask. How can i get a LigParGen or something else? Is it addons for GROMACS?

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**Author:** ![TomPiggot](https://avatars.discourse-cdn.com/v4/letter/t/77aa72/32.png) [@TomPiggot](https://gromacs.bioexcel.eu/u/TomPiggot)\
**Post date:** [October 27, 2022, 7:42pm UTC](https://gromacs.bioexcel.eu/t/system-optimization/5121/8 "2022-10-27T19:42:42Z")

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With developing force field parameters for your molecule I’d suggest having a good look at the AMBER-DYES and CHARMM-DYES parameters and papers. This sort of molecule isn’t the easiest to model accurately with atomistic force fields.

Cheers

Tom

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<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:** [October 27, 2022, 7:51pm UTC](https://gromacs.bioexcel.eu/t/system-optimization/5121/9 "2022-10-27T19:51:46Z")

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> [@vadiambos](#):
>
> Forgot to ask. How can i get a LigParGen or something else? Is it addons for GROMACS?

Ask Google :)