# Error in protein RNA docking

**URL:** <https://ask.bioexcel.eu/t/error-in-protein-rna-docking/2001>\
**Category:** HADDOCK\
**Created:** [May 7, 2020, 2:04pm UTC](https://ask.bioexcel.eu/t/error-in-protein-rna-docking/2001 "2020-05-07T14:04:21Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![vikramdalal](https://avatars.discourse-cdn.com/v4/letter/v/54ee81/32.png) [@vikramdalal](https://ask.bioexcel.eu/u/vikramdalal)\
**Post date:** [May 7, 2020, 2:04pm UTC](https://ask.bioexcel.eu/t/error-in-protein-rna-docking/2001/1 "2020-05-07T14:04:21Z")

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Hello Everyone,

I have to do protein-RNA docking.  
I have mentioned the 3 letters code for RNA as:-  
A- ADE  
C-CYT  
G-GUA  
U-URA

I am getting following error message:-

There was an error in the processing of the data. Your have been notified by email about the possible cause.

Any help or suggestions to resolve this issue will be highly appreciated.

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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:** [May 7, 2020, 2:18pm UTC](https://ask.bioexcel.eu/t/error-in-protein-rna-docking/2001/2 "2020-05-07T14:18:00Z")

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Using the 2.2 web server?

URA should be URI

And did you define the molecule correctly as RNA?

Also it sometimes help to read the PDB in for example PyMol and save it again as PDB format.

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<div class="post-metadata">

**Author:** ![vikramdalal](https://avatars.discourse-cdn.com/v4/letter/v/54ee81/32.png) [@vikramdalal](https://ask.bioexcel.eu/u/vikramdalal)\
**Post date:** [May 7, 2020, 4:03pm UTC](https://ask.bioexcel.eu/t/error-in-protein-rna-docking/2001/3 "2020-05-07T16:03:15Z")

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Thank you for your valuable suggestions.  
I think may be problem is with the 3D structure of RNA.  
I am new to protein-RNA docking.

How can I predict the reliable 3D model of RNA which can be directly used for protein-RNA docking in HADDOCK.

Thank you in advance

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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:** [May 8, 2020, 6:27pm UTC](https://ask.bioexcel.eu/t/error-in-protein-rna-docking/2001/4 "2020-05-08T18:27:42Z")

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Reliable 3D models of RNA is a hard to get… It all depends on the size.  
And I can’t really point you to some server for this.

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**Author:** ![honoratorv](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/honoratorv/32/672_2.png) [@honoratorv](https://ask.bioexcel.eu/u/honoratorv)\
**Post date:** [May 9, 2020, 6:55am UTC](https://ask.bioexcel.eu/t/error-in-protein-rna-docking/2001/5 "2020-05-09T06:55:08Z")

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RNA modelling is not a trivial task, it will require some experience with modelling methods as well as a good understanding of the RNA molecule itself. The following could be good starting points:

- [https://simtk.org/projects/nast](https://simtk.org/projects/nast)
- [http://www.biomath.nyu.edu/?q=software/RAGTOP](http://www.biomath.nyu.edu/?q=software/RAGTOP)
- [https://sourceforge.net/projects/barnacle-rna](https://sourceforge.net/projects/barnacle-rna)

Good luck! 🙂