# Parameters for RNA-ligand docking

**URL:** <https://ask.bioexcel.eu/t/parameters-for-rna-ligand-docking/4403>\
**Category:** HADDOCK\
**Created:** [July 6, 2023, 11:20am UTC](https://ask.bioexcel.eu/t/parameters-for-rna-ligand-docking/4403 "2023-07-06T11:20:58Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![LFT](https://avatars.discourse-cdn.com/v4/letter/l/34f0e0/32.png) [@LFT](https://ask.bioexcel.eu/u/LFT)\
**Post date:** [July 6, 2023, 11:20am UTC](https://ask.bioexcel.eu/t/parameters-for-rna-ligand-docking/4403/1 "2023-07-06T11:20:58Z")

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I would like to study the binding of different aptamers ( **RNA sequences** ) to the **ligand** PFOA. Haddock allows me to do so, but I don’t know how to tune the **parameters** to optimize the results, and cannot find any information anywhere. I would really appreciate if someone could give me some notions about how to find the best parameters to perform Haddock in this case. Thanks!

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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:** [July 7, 2023, 12:18pm UTC](https://ask.bioexcel.eu/t/parameters-for-rna-ligand-docking/4403/2 "2023-07-07T12:18:11Z")

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Wee never benchmarked RNA-ligand docking but did some yet unpublished work on DNA-ligand modelling. Here is a matrix of parameters (the last column should work for RNA-ligand modelling):

| | | **default value** | **Protein/Small molecule** | **Protein/DNA** | **DNA/small molecule** |
| --- | --- | --- | --- | --- | --- |
| **Dieletric constant for it0** | dielec\_0 | rdie | cdie | rdie | **cdie** |
| **Dieletric constant for it1** | dielec\_1 | rdie | cdie | rdie | **cdie** |
| **MD steps for rigid body high temperature TAD** | initiosteps | 500 | 0 | 500 | **0** |
| **MD steps during first rigid body cooling stage** | cool1\_steps | 500 | 0 | 500 | **0** |
| **Initial temperature for second TAD cooling step with flexible side-chain at the interface** | tadinit2\_t | 1000 | 500 | 1000 | **500** |
| **Initial temperature for third TAD cooling step with fully flexible interface** | tadinit3\_t | 1000 | 300 | 1000 | **300** |
| **Weight of the intermolecular van der Waals energy for scoring at the rigid-body docking stage** | w\_vdw\_0 | 0.01 | 1 | 0.01 | **1** |
| **Weight of the intermolecular electrostatic energy for scoring at the final stage** | w\_elec\_2 | 0.2 | 0.1 | 0.2 | **0.1** |
| **Dielectric constant for rigid-body docking** | epsilon\_0 | 10 | 10 | 78 | **78** |
| **Dielectric constant for the semi-flexible refinement** | epsilon\_1 | 10 | 10 | 78 | **10** |

And in addition you might consider setting the weight of the desolation energy term in the scoring function to 0

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<div class="post-metadata">

**Author:** ![LFT](https://avatars.discourse-cdn.com/v4/letter/l/34f0e0/32.png) [@LFT](https://ask.bioexcel.eu/u/LFT)\
**Post date:** [July 11, 2023, 9:37am UTC](https://ask.bioexcel.eu/t/parameters-for-rna-ligand-docking/4403/3 "2023-07-11T09:37:55Z")

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Thank you so much!