# Dimer dissolved / splited during docking
**URL:** https://ask.bioexcel.eu/t/dimer-dissolved-splited-during-docking/1779
**Category:** HADDOCK
**Created:** [December 25, 2019, 2:58am UTC](https://ask.bioexcel.eu/t/dimer-dissolved-splited-during-docking/1779 "2019-12-25T02:58:15Z")
**Posts on this page:** 7
**Page:** 1
### Author:  [@kin](https://ask.bioexcel.eu/u/kin)
#### Post date: [December 25, 2019, 2:58am UTC](https://ask.bioexcel.eu/t/dimer-dissolved-splited-during-docking/1779/1 "2019-12-25T02:58:15Z")
I was docking a homolog model dimer protein (swissmodel) with peptide ligand and the dimer splitted apart. Previously when i was using the exprimental xray crystallography structure to screen for optimal parameters, they never split into discrete chains. Anyone encountered similar issues? Please help thanks.
This is my homolog model
[DRA00201\_DRB00101\_renumbered.pdb](https://europe1.discourse-cdn.com/flex013/uploads/bioexcel/original/1X/eb2fd70541ea133576c1cd6679022f3a0ef94fab.pdb) (236.4 KB)
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### Author:  [@honoratorv](https://ask.bioexcel.eu/u/honoratorv)
#### Post date: [December 25, 2019, 2:48pm UTC](https://ask.bioexcel.eu/t/dimer-dissolved-splited-during-docking/1779/2 "2019-12-25T14:48:22Z")
Could you please share the link of the HADDOCK run?
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### Author:  [@kin](https://ask.bioexcel.eu/u/kin)
#### Post date: [December 25, 2019, 3:08pm UTC](https://ask.bioexcel.eu/t/dimer-dissolved-splited-during-docking/1779/3 "2019-12-25T15:08:45Z")
THanks for the prompt reply, please refer to below for the link
[https://milou.science.uu.nl/serviceresults/HADDOCK2.2/6851440797/HLADRA00201\_DRB00101\_2000rigidrun\_32Hbond\_1/](https://milou.science.uu.nl/serviceresults/HADDOCK2.2/6851440797/HLADRA00201_DRB00101_2000rigidrun_32Hbond_1/)
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### Author:  [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)
#### Post date: [December 25, 2019, 10:44pm UTC](https://ask.bioexcel.eu/t/dimer-dissolved-splited-during-docking/1779/4 "2019-12-25T22:44:19Z")
Since your dimer is a model, it could well be there are clashes that cause the models to separate. You could try refining it first using the refinement interface and defining each monomer as one molecule
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### Author:  [@kin](https://ask.bioexcel.eu/u/kin)
#### Post date: [December 26, 2019, 1:52am UTC](https://ask.bioexcel.eu/t/dimer-dissolved-splited-during-docking/1779/5 "2019-12-26T01:52:24Z")
thanks for the respond. may i know how to define each monomer as one molecule? And please recommend any structure refinement interface. thanks
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### Author:  [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)
#### Post date: [December 26, 2019, 12:35pm UTC](https://ask.bioexcel.eu/t/dimer-dissolved-splited-during-docking/1779/6 "2019-12-26T12:35:25Z")
Split the file into two (one file per monomer)
And submit it to the HADDOCK refinement interface:
[https://haddock.science.uu.nl/services/HADDOCK2.2/haddockserver-refinement.html](https://haddock.science.uu.nl/services/HADDOCK2.2/haddockserver-refinement.html)
(you do need expert access for this - request it online in your registration page)
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### Author:  [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)
#### Post date: [December 28, 2019, 8:36am UTC](https://ask.bioexcel.eu/t/dimer-dissolved-splited-during-docking/1779/8 "2019-12-28T08:36:32Z")
The server simply doesn’t support refinement of a single molecule - it is meant for complexes