# Ligand modelled in Avogadro "contains multiple residues with number 1 in chain or duplicated atom names."

**URL:** https://ask.bioexcel.eu/t/ligand-modelled-in-avogadro-contains-multiple-residues-with-number-1-in-chain-or-duplicated-atom-names/4425
**Category:** HADDOCK
**Created:** [July 24, 2023, 12:12am UTC](https://ask.bioexcel.eu/t/ligand-modelled-in-avogadro-contains-multiple-residues-with-number-1-in-chain-or-duplicated-atom-names/4425 "2023-07-24T00:12:59Z")
**Posts on this page:** 3
**Page:** 1

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### Author: ![bashok](https://avatars.discourse-cdn.com/v4/letter/b/57b2e6/32.png) [@bashok](https://ask.bioexcel.eu/u/bashok)
#### Post date: [July 24, 2023, 12:12am UTC](https://ask.bioexcel.eu/t/ligand-modelled-in-avogadro-contains-multiple-residues-with-number-1-in-chain-or-duplicated-atom-names/4425/1 "2023-07-24T00:12:59Z")

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Hi all, I’m using HADDOCK to dock two proteins and a ligand (MS4077) to model a ternary complex. Initially I was unable to get the 2nd protein to work but used PDBTools “setaltloc” and was able to get the protein-protein complex without MS4077 to dock successfully with HADDOCK. Now I am trying to dock all three molecules but the ligand (molecule 3) is giving me the error: “Error in PDB file. Your PDB contains multiple residues with number 1 in chain or duplicated atom names.”

I’ve already tried using PDBTools “uniqname” and “setaltloc” seperately but it deletes most of the ligand. I also tried another method of using the text editor to change the atom names to C1, C2, C3, O1… etc. as per another thread on bioexcel but that also did not work. As I am a new user I cannot upload the file, but any help would be appreciated. Thank you!

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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: [July 24, 2023, 7:01am UTC](https://ask.bioexcel.eu/t/ligand-modelled-in-avogadro-contains-multiple-residues-with-number-1-in-chain-or-duplicated-atom-names/4425/2 "2023-07-24T07:01:43Z")

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You ligand must have unique atom names.

Edit and check carefully the PDB file.

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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: [July 24, 2023, 8:03am UTC](https://ask.bioexcel.eu/t/ligand-modelled-in-avogadro-contains-multiple-residues-with-number-1-in-chain-or-duplicated-atom-names/4425/3 "2023-07-24T08:03:28Z")

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Thanks for reaching out with this question.

Please have a look in our [HADDOCK FAQ](https://bianca.science.uu.nl/haddock2.4/faq) and let us know if that solved your issue! 🙂