# Is there a tutorial for a ligand + cofactor + receptor system?

**URL:** <https://gromacs.bioexcel.eu/t/is-there-a-tutorial-for-a-ligand-cofactor-receptor-system/2423>\
**Category:** User discussions\
**Created:** [June 29, 2021, 2:37pm UTC](https://gromacs.bioexcel.eu/t/is-there-a-tutorial-for-a-ligand-cofactor-receptor-system/2423 "2021-06-29T14:37:27Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![patc](https://avatars.discourse-cdn.com/v4/letter/p/9fc29f/32.png) [@patc](https://gromacs.bioexcel.eu/u/patc)\
**Post date:** [June 29, 2021, 2:37pm UTC](https://gromacs.bioexcel.eu/t/is-there-a-tutorial-for-a-ligand-cofactor-receptor-system/2423/1 "2021-06-29T14:37:28Z")

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hello guys. I am trying to get into MD, however i am struggling to go beyond the tutorials that are already around. there is this tutorial:

[http://www.mdtutorials.com/gmx/](http://www.mdtutorials.com/gmx/)

which describes a ligand-receptor complex. however, what if i have multiple ligands? i can just keep adding them to the topology, but then how do i constrain them?  
thank you in advance

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**Author:** ![mbernhardt](https://avatars.discourse-cdn.com/v4/letter/m/ecccb3/32.png) [@mbernhardt](https://gromacs.bioexcel.eu/u/mbernhardt)\
**Post date:** [July 1, 2021, 9:36am UTC](https://gromacs.bioexcel.eu/t/is-there-a-tutorial-for-a-ligand-cofactor-receptor-system/2423/2 "2021-07-01T09:36:55Z")

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I have never seen such a tutorial. I’m not a specialist with proteins. My guess is that one would try to test binding with and without the cofactor present. But better you have a look into literature and find papers where people simulate protein + ligand + cofactor.

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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:** [July 3, 2021, 5:05pm UTC](https://gromacs.bioexcel.eu/t/is-there-a-tutorial-for-a-ligand-cofactor-receptor-system/2423/3 "2021-07-03T17:05:24Z")

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The approach is the same, the only modification would be that if both non-standard entities require the introduction of new parameters or atom types, those have to be collated into a single file before any molecule topology can be `#included` in the system `.top` file. All force field parameters have to be known before any molecule can be defined.

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**Author:** ![patc](https://avatars.discourse-cdn.com/v4/letter/p/9fc29f/32.png) [@patc](https://gromacs.bioexcel.eu/u/patc)\
**Post date:** [July 5, 2021, 2:01pm UTC](https://gromacs.bioexcel.eu/t/is-there-a-tutorial-for-a-ligand-cofactor-receptor-system/2423/4 "2021-07-05T14:01:59Z")

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thank you for the reply! i managed to get it running like that. i put the ligand atoms into an atoms.itp, that i included before the molecule types and that allowed me to run it just fine!