# Protein-ligand docking

**URL:** https://ask.bioexcel.eu/t/protein-ligand-docking/58
**Category:** HADDOCK
**Created:** [April 11, 2016, 11:58am UTC](https://ask.bioexcel.eu/t/protein-ligand-docking/58 "2016-04-11T11:58:46Z")
**Posts on this page:** 1
**Showing post:** 27

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### Author: ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)
#### Post date: [April 18, 2019, 2:47pm UTC](https://ask.bioexcel.eu/t/protein-ligand-docking/58/27 "2019-04-18T14:47:54Z")

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Hi Juliet

Two issues:

1. The error message reports the presence of multiple conformations of some residues in your crystal structure. You will have to select which one to use. This can be done for example with our `pdb-tools`

See for example in the HADDOCK forum: [Haddock server problem](https://ask.bioexcel.eu/t/haddock-server-problem/591)

1. HADDOCK does support a number of modified amino acids, but they need to have the proper naming. The list of supported modified amino acids can be found at:

In your case, an acetylated LYS should be named `ALY` instead of `LYS` in the PDB file

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