# Docked proteins are separated

**URL:** <https://ask.bioexcel.eu/t/docked-proteins-are-separated/1635>\
**Category:** HADDOCK\
**Created:** [August 13, 2019, 8:38pm UTC](https://ask.bioexcel.eu/t/docked-proteins-are-separated/1635 "2019-08-13T20:38:25Z")\
**Posts on this page:** 6\
**Page:** 1

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**Author:** ![hengameh\_shams](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/hengameh_shams/32/187_2.png) [@hengameh\_shams](https://ask.bioexcel.eu/u/hengameh_shams)\
**Post date:** [August 13, 2019, 8:38pm UTC](https://ask.bioexcel.eu/t/docked-proteins-are-separated/1635/1 "2019-08-13T20:38:26Z")

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Hello,

I submitted a dimer as the receptor and a single chain protein as the ligand using the easy interface. Docking was finished successfully and scores and interaction energies seem normal. However, when I visualize the clusters in VMD, proteins are separated in space. I tried searching the manual and tools but couldn’t find any similar issues. Could you kindly help me fix it?

I really appreciate your help.

Best Regards

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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:** [August 14, 2019, 6:49am UTC](https://ask.bioexcel.eu/t/docked-proteins-are-separated/1635/2 "2019-08-14T06:49:40Z")

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Is your dimer separated in space? Or the dimer with the other protein?

Did you renumber the dimer to avoid overlap in numbering?

Are you using a local version of HADDOCK or the web server?

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<div class="post-metadata">

**Author:** ![hengameh\_shams](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/hengameh_shams/32/187_2.png) [@hengameh\_shams](https://ask.bioexcel.eu/u/hengameh_shams)\
**Post date:** [August 14, 2019, 6:53am UTC](https://ask.bioexcel.eu/t/docked-proteins-are-separated/1635/3 "2019-08-14T06:53:13Z")

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Dimer with the other protein.

Yes, I did.

I used the web server.

Thanks.

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<div class="post-metadata">

**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:** [August 14, 2019, 7:08am UTC](https://ask.bioexcel.eu/t/docked-proteins-are-separated/1635/4 "2019-08-14T07:08:10Z")

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Then most likely a problem with your restraints I would say. Can you share (via email) the link to your result page?

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<div class="post-metadata">

**Author:** ![hengameh\_shams](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/hengameh_shams/32/187_2.png) [@hengameh\_shams](https://ask.bioexcel.eu/u/hengameh_shams)\
**Post date:** [August 14, 2019, 7:09am UTC](https://ask.bioexcel.eu/t/docked-proteins-are-separated/1635/5 "2019-08-14T07:09:14Z")

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Sure, which email address? Thanks!

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<div class="post-metadata">

**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:** [August 15, 2019, 11:32am UTC](https://ask.bioexcel.eu/t/docked-proteins-are-separated/1635/6 "2019-08-15T11:32:01Z")

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E.g. [haddock.support@gmail.com](mailto:haddock.support@gmail.com)