# Docking of small ssDNA on proteins

**URL:** <https://ask.bioexcel.eu/t/docking-of-small-ssdna-on-proteins/6183>\
**Category:** HADDOCK\
**Created:** [June 29, 2026, 2:49pm UTC](https://ask.bioexcel.eu/t/docking-of-small-ssdna-on-proteins/6183 "2026-06-29T14:49:43Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![BioMarc](https://avatars.discourse-cdn.com/v4/letter/b/58f4c7/32.png) [@BioMarc](https://ask.bioexcel.eu/u/BioMarc)\
**Post date:** [June 29, 2026, 2:49pm UTC](https://ask.bioexcel.eu/t/docking-of-small-ssdna-on-proteins/6183/1 "2026-06-29T14:49:43Z")

</div>

Hello,

I am trying to do a docking of multiple small (6 nts) single-stranded DNAs on a protein. I am wondering if I am using the right parameters. I would like to dock blindly. Here is a part of my cfg file with the parameters i found online.

[topoaa]  
autohis = true

[rigidbody]  
tolerance = 5  
ambig\_fname = “”  
sampling = 10000  
surfrest = true  
epsilon = 78  
dielec = “cdie”   
randremoval = false  
w\_desolv = 0

[caprieval]

[seletop]  
select = 400

[flexref]  
tolerance = 5  
ambig\_fname = “”  
epsilon = 78  
dielec = “cdie”  
randremoval = false  
w\_desolv = 0  
dnarest\_on = false  
tadfactor = 4

[caprieval]

[emref]  
tolerance = 5  
ambig\_fname = “”  
randremoval = false  
dnarest\_on = false  
w\_desolv = 0  
contactairs = true

[caprieval]

[emscoring]

[caprieval]

Thanks you very much,

Marc-Antoine

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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:** [June 29, 2026, 3:15pm UTC](https://ask.bioexcel.eu/t/docking-of-small-ssdna-on-proteins/6183/2 "2026-06-29T15:15:37Z")

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A few suggested changes (and you might consider adding some clustering step at the end)

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<div class="post-metadata">

**Author:** ![BioMarc](https://avatars.discourse-cdn.com/v4/letter/b/58f4c7/32.png) [@BioMarc](https://ask.bioexcel.eu/u/BioMarc)\
**Post date:** [June 29, 2026, 3:32pm UTC](https://ask.bioexcel.eu/t/docking-of-small-ssdna-on-proteins/6183/3 "2026-06-29T15:32:45Z")

</div>

Hello @amjjbonvin,

Thanks for the answers, but I don’t see your suggested changes.

Thanks again,

Marc-Antoine

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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:** [June 29, 2026, 9:01pm UTC](https://ask.bioexcel.eu/t/docking-of-small-ssdna-on-proteins/6183/4 "2026-06-29T21:01:01Z")

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Must have been filtered out from my email answer… Here it comes:

#=====================

[topoaa]

[rigidbody]  
tolerance = 5  
sampling = 10000  
**cmrest = true**  
epsilon = 78  
dielec = “cdie”  
w\_desolv = 0

[caprieval]

[seletop]

select = 400

[flexref]  
tolerance = 5  
epsilon = 78  
dielec = “cdie”  
w\_desolv = 0

**contactairs = true**

tadfactor = 4

[caprieval]

[emref]  
tolerance = 5  
w\_desolv = 0

[caprieval]

#=====================