# How to simulate two ligands? My setup doesnt include any polypeptide

**URL:** <https://gromacs.bioexcel.eu/t/how-to-simulate-two-ligands-my-setup-doesnt-include-any-polypeptide/2297>\
**Category:** User discussions\
**Tags:** mdp-parameters, mdrun, simulation-setup\
**Created:** [June 4, 2021, 5:49pm UTC](https://gromacs.bioexcel.eu/t/how-to-simulate-two-ligands-my-setup-doesnt-include-any-polypeptide/2297 "2021-06-04T17:49:39Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![pateldhaval.in](https://avatars.discourse-cdn.com/v4/letter/p/f6c823/32.png) [@pateldhaval.in](https://gromacs.bioexcel.eu/u/pateldhaval.in)\
**Post date:** [June 4, 2021, 5:49pm UTC](https://gromacs.bioexcel.eu/t/how-to-simulate-two-ligands-my-setup-doesnt-include-any-polypeptide/2297/1 "2021-06-04T17:49:39Z")

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GROMACS version:  
GROMACS modification: Yes/No  
Here post your question  
How can one simulate two ligands? I have a crown ether molecule and another small ligand which is trapped in the crown. Later i plan to study the umbrella sampling for the same.

How can we generate topology files for the above simulation setup?  
Any help will be appreciated

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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:** [June 5, 2021, 3:36am UTC](https://gromacs.bioexcel.eu/t/how-to-simulate-two-ligands-my-setup-doesnt-include-any-polypeptide/2297/2 "2021-06-05T03:36:28Z")

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In short, you have to manually write the topology. If you already have suitable topologies for both within the framework of an existing force field, it **may** be as simple as:

```
#include "parent.ff/forcefield.itp"
#include "crown_ether.itp"
#include "ligand.itp"
[system]
my system
[molecules]
crown_ether 1
ligand 1
```

If your topologies introduce new atom types or other parameters, those will have to be suitably grouped before any `[moleculetype]` can be introduced (see recent threads on exactly this topic).

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<div class="post-metadata">

**Author:** ![pateldhaval.in](https://avatars.discourse-cdn.com/v4/letter/p/f6c823/32.png) [@pateldhaval.in](https://gromacs.bioexcel.eu/u/pateldhaval.in)\
**Post date:** [July 2, 2021, 6:49pm UTC](https://gromacs.bioexcel.eu/t/how-to-simulate-two-ligands-my-setup-doesnt-include-any-polypeptide/2297/3 "2021-07-02T18:49:28Z")

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Thank you for your response. I will try and get back to you in case of any query