# MDtutorial ligand restraints: Cannot use restrained groups for this system

**URL:** <https://gromacs.bioexcel.eu/t/mdtutorial-ligand-restraints-cannot-use-restrained-groups-for-this-system/8926>\
**Category:** User discussions\
**Tags:** mdrun, simulation-setup\
**Created:** [April 19, 2024, 1:02am UTC](https://gromacs.bioexcel.eu/t/mdtutorial-ligand-restraints-cannot-use-restrained-groups-for-this-system/8926 "2024-04-19T01:02:42Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![effy](https://avatars.discourse-cdn.com/v4/letter/e/9fc348/32.png) [@effy](https://gromacs.bioexcel.eu/u/effy)\
**Post date:** [April 19, 2024, 1:02am UTC](https://gromacs.bioexcel.eu/t/mdtutorial-ligand-restraints-cannot-use-restrained-groups-for-this-system/8926/1 "2024-04-19T01:02:42Z")

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GROMACS version:2024.1  
GROMACS modification: No

Hi all,

I’m following the tutorial on Protein Ligand Complex by Dr. Lemkul and I encountered a problem with restraining the ligand. [Protein-Ligand Complex](http://www.mdtutorials.com/gmx/complex/06_equil.html)

I followed the instructions and first restrained the H atoms on JZ4. Then I added restrain infomation at the end of topology file. I then grouped protein with ligand. Protein\_JZ4 group appeared on my index.ndx file. So I procceeded with NVT equilibration steps, but this message showed up when I ran gmx mdrun -v -deffnm nvt: Update groups can not be used for this system because atoms that are (in)directly constrained together are interdispersed with other atoms. I tried to group multiple times but the message still showed up. Could anyone let me know what’s going on and how to fix it please? Thanks!

 ![image](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/c/cefa81a572f69f92effd69818bd2cab0c2d1c25d.png)

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<div class="post-metadata">

**Author:** ![scinikhil](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/scinikhil/32/3483_2.png) [@scinikhil](https://gromacs.bioexcel.eu/u/scinikhil)\
**Post date:** [April 19, 2024, 4:02am UTC](https://gromacs.bioexcel.eu/t/mdtutorial-ligand-restraints-cannot-use-restrained-groups-for-this-system/8926/2 "2024-04-19T04:02:29Z")

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check the index and make sure there is no mixing of atoms with other index groups