# Can the haddock be used to tackle the RNA-RNA systems?

**URL:** <https://ask.bioexcel.eu/t/can-the-haddock-be-used-to-tackle-the-rna-rna-systems/1318>\
**Category:** HADDOCK\
**Created:** [December 8, 2018, 6:43am UTC](https://ask.bioexcel.eu/t/can-the-haddock-be-used-to-tackle-the-rna-rna-systems/1318 "2018-12-08T06:43:24Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Yikan\_Zhang](https://avatars.discourse-cdn.com/v4/letter/y/da6949/32.png) [@Yikan\_Zhang](https://ask.bioexcel.eu/u/Yikan_Zhang)\
**Post date:** [December 8, 2018, 6:43am UTC](https://ask.bioexcel.eu/t/can-the-haddock-be-used-to-tackle-the-rna-rna-systems/1318/1 "2018-12-08T06:43:24Z")

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The HADDOCK category is meant to discuss any HADDOCK-related issue. For general information about HADDOCK refer to [http://www.bonvinlab.org/software/haddock2.2](http://www.bonvinlab.org/software/haddock2.2)

I have two RNAs and they may have some interactive points determined by ITC. So, I want to model the RNA complexes by haddock. Does that make sense? If do, how can I specify the base pair interaction between them(in the docking, for example: between A: 14G 15C 16A and B: 33U 34G 35C)?

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**Author:** ![Adrimel](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/adrimel/32/40_2.png) [@Adrimel](https://ask.bioexcel.eu/u/Adrimel)\
**Post date:** [December 13, 2018, 9:04am UTC](https://ask.bioexcel.eu/t/can-the-haddock-be-used-to-tackle-the-rna-rna-systems/1318/2 "2018-12-13T09:04:28Z")

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Dear Yikan,

In principle it can be done. Simply specify RNA as molecule and make sure you are using a 3 letter code for the residue names.

To learn how to define restraints in CNS format (or define active residues), please check our tutorials and/or refer to our Nature Protocol 2010 paper where we provide examples

Regards,  
Adrien