# Local HADDOCK3 missing ligands

**URL:** https://ask.bioexcel.eu/t/local-haddock3-missing-ligands/4346
**Category:** HADDOCK
**Created:** [May 24, 2023, 4:25am UTC](https://ask.bioexcel.eu/t/local-haddock3-missing-ligands/4346 "2023-05-24T04:25:36Z")
**Posts on this page:** 1
**Showing post:** 10

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### Author: ![honoratorv](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/honoratorv/32/672_2.png) [@honoratorv](https://ask.bioexcel.eu/u/honoratorv)
#### Post date: [May 26, 2023, 8:30am UTC](https://ask.bioexcel.eu/t/local-haddock3-missing-ligands/4346/10 "2023-05-26T08:30:01Z")

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> [@zoeyxyang](#):
>
> **PRODGR** mentioned in the tutorial seems to be down.

Thanks for pointing this out, I tried to look for a new site but could not find anything - we’ll reach out to them and ask if where the domain has moved.

> [@zoeyxyang](#):
>
> Suppose I get the ligand.top and ligand.param files, do I still need to keep the ligand information in the pdb file of the protein where the ligand is attached to?

Each of these files describe different things so that CNS (the molecular engine used by Haddock) can interpret the molecule; the topology represents what are the atomic types and their properties (mass, charge), the parameters are a description of the values that should be used for the inter and intra-molecular calculations, the pdb itself described the spatial cordinates of the atoms. So indeed you need all of them.

> [@zoeyxyang](#):
>
> Would these files generated from the results of HADDOCK2.4 server be the correct input files for the ligand on my protein?

Yes they should! I’ve updated the server so that once you click the `Download input files`, you will also get the PRODRG generated topologies and parameters. From there what you need to do is feed these files into your `toml` configuration for haddock3:

```toml
ligand_param_fname = "/path/to/the/data/ligand.par"
ligand_top_fname = "/path/to/the/data/ligand.top"

```

You can use this [docking-protein-ligand-full.toml](https://raw.githubusercontent.com/haddocking/haddock3/main/examples/docking-protein-ligand/docking-protein-ligand-full.cfg) as a template for your setup.

Good luck!

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