# Single Stranded DNA Flexibility
**URL:** https://ask.bioexcel.eu/t/single-stranded-dna-flexibility/5009
**Category:** HADDOCK
**Created:** [May 14, 2024, 3:29pm UTC](https://ask.bioexcel.eu/t/single-stranded-dna-flexibility/5009 "2024-05-14T15:29:00Z")
**Posts on this page:** 4
**Page:** 1
### Author:  [@ChapepperoniPizza](https://ask.bioexcel.eu/u/ChapepperoniPizza)
#### Post date: [May 14, 2024, 3:29pm UTC](https://ask.bioexcel.eu/t/single-stranded-dna-flexibility/5009/1 "2024-05-14T15:29:00Z")
Hi all. I have been attempting to dock a dimeric protein to single stranded DNA. I have assigned the entire DNA molecule as flexible but I see no conformation changes between the input PDB and the modeling output. I am using the webserver and the DNA was created simply using the FNAB command in PyMol and editing the HETATM tags in the text file. Any advice on why my molecule is showing no flexibility? I fed no restraints, and instead am using ambiguous docking.
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### Author:  [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)
#### Post date: [May 15, 2024, 9:28am UTC](https://ask.bioexcel.eu/t/single-stranded-dna-flexibility/5009/2 "2024-05-15T09:28:51Z")
Did you define the DNA as fully flexible?
And without specific restraints, I would not expect any significant conformational changes… Did you turn on the center of mass restraints? Or what do you mean by “using ambiguous docking”?
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### Author:  [@ChapepperoniPizza](https://ask.bioexcel.eu/u/ChapepperoniPizza)
#### Post date: [May 15, 2024, 2:09pm UTC](https://ask.bioexcel.eu/t/single-stranded-dna-flexibility/5009/3 "2024-05-15T14:09:06Z")
I can send param file if it’d be helpful, but essentially we have assigned the surface of our dimeric protein as automatically passive, and the DNA has been assigned ten active nucleotides at the center of its sequence. The entire DNA molecule was marked as fully flexible.
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### Author:  [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)
#### Post date: [May 15, 2024, 3:02pm UTC](https://ask.bioexcel.eu/t/single-stranded-dna-flexibility/5009/4 "2024-05-15T15:02:23Z")
Did you also define your DNA as fully flexible?
Can you share a link to a run (if you have used the server)?
You can also sent it by email.