# Selecting interacting residue for docking **URL:** \ **Category:** HADDOCK\ **Created:** [April 4, 2017, 7:12pm UTC](https://ask.bioexcel.eu/t/selecting-interacting-residue-for-docking/338 "2017-04-04T19:12:47Z")\ **Posts on this page:** 10\ **Page:** 1
**Author:** ![diffracteD](https://avatars.discourse-cdn.com/v4/letter/d/958977/32.png) [@diffracteD](https://ask.bioexcel.eu/u/diffracteD)\ **Post date:** [April 4, 2017, 7:12pm UTC](https://ask.bioexcel.eu/t/selecting-interacting-residue-for-docking/338/1 "2017-04-04T19:12:47Z")
I have a DNA structure (22 residue) and have synthesized a small ligand molecule that is supposed to interact with the DNA (as per my other experiments). Now, what I’m trying to achieve is to dock the ligand into the DNA to get a structural insight regarding the interaction sites. In such a scenario (I’m running Prediction mode) what am I supposed to mention in interacting residue column for both DNA and ligand ? Is it 1,2,3,4,5,6,7,…,22 for DNA and 1 for ligand ? Please help me out here. I’m a newbie to this package. ---
**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:** [April 5, 2017, 8:14am UTC](https://ask.bioexcel.eu/t/selecting-interacting-residue-for-docking/338/2 "2017-04-05T08:14:16Z")
I assume you have no idea where the ligand might bind on your DNA? In that case you might consider following our ligand docking tutorial. Check > **[HADDOCK small molecule binding site screening](http://www.bonvinlab.org/education/HADDOCK-binding-sites/)** > > A small tutorial on identifying putative binding site for small ligands using HADDOCK ---
**Author:** ![diffracteD](https://avatars.discourse-cdn.com/v4/letter/d/958977/32.png) [@diffracteD](https://ask.bioexcel.eu/u/diffracteD)\ **Post date:** [April 5, 2017, 8:18am UTC](https://ask.bioexcel.eu/t/selecting-interacting-residue-for-docking/338/3 "2017-04-05T08:18:28Z")
Thank you for the tutorial link. Yes. The ligand is newly synthesized. That’s why I’m trying the Prediction mode in the webserver. ---
**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:** [April 5, 2017, 8:27am UTC](https://ask.bioexcel.eu/t/selecting-interacting-residue-for-docking/338/4 "2017-04-05T08:27:42Z")
PS: You don’t need the prediction interface for this. Rather follow the tutorial I would say ---
**Author:** ![diffracteD](https://avatars.discourse-cdn.com/v4/letter/d/958977/32.png) [@diffracteD](https://ask.bioexcel.eu/u/diffracteD)\ **Post date:** [April 7, 2017, 7:16am UTC](https://ask.bioexcel.eu/t/selecting-interacting-residue-for-docking/338/5 "2017-04-07T07:16:06Z")
I was trying to follow the tutorial you mentioned. I’m getting the following error there: “There was an inconsistency in your data Error message Manual restraints and random patches are mutually exclusive” PDB formatting is correct this time, i hope, as Prediction mode run completed successfully. Would you please help me out here ? I followed the tutorial restraining parameters as mentioned there. ---
**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:** [April 7, 2017, 7:36am UTC](https://ask.bioexcel.eu/t/selecting-interacting-residue-for-docking/338/6 "2017-04-07T07:36:42Z")
You can not specify AIRs or provide restraints together with random patches - as the error message it telling you. The tutorial does not do that. ---
**Author:** ![diffracteD](https://avatars.discourse-cdn.com/v4/letter/d/958977/32.png) [@diffracteD](https://ask.bioexcel.eu/u/diffracteD)\ **Post date:** [April 7, 2017, 7:42am UTC](https://ask.bioexcel.eu/t/selecting-interacting-residue-for-docking/338/7 "2017-04-07T07:42:33Z")
Yes, but if I leave active and passive residues blank then I’m facing following crash: There was an error in the authorization routine of the server Full error information: Traceback (most recent call last): File “/home/enmr/services-enmr/HADDOCK2.2/py/haddockserver.py”, line 307, in serve\_haddock dd2 = newmodel.convert(auth).convert(HaddockGuruInterface).convert(HaddockMultiRunParameters) File “haddock::HaddockGuruInterface.spy”, line 3629, in convert c = spyder.core.convert(HaddockGuruInterface, target, self, deepcopy) File “spyder.modules.core::pathing.py”, line 267, in convert ret = do\_convert(i,o,arg) File “spyder.modules.core::pathing.py”, line 254, in do\_convert conv = execute\_path(i,arg,path,failed,visited,None,0,None) File “spyder.modules.core::pathing.py”, line 156, in execute\_path result = spyder. **types** c.outtype File “haddock::HaddockEasyInterface.spy”, line 140, in **init** HaddockEasyInterface. **dict** [HaddockEasyInterface. **constructor**](self, \*args, \*\*args2) File “haddock::HaddockEasyInterface.spy”, line 247, in constructor\_fromany self.validate() File “haddock::HaddockEasyInterface.spy”, line 384, in validate self. **validate** () File “haddock::HaddockEasyInterface.spy”, line 405, in **validate** if not has\_r1: spyder.core.\_raise(self, ‘HaddockValidationError(“You must supply active and/or passive residues for your first protein.”)’, ‘if not has\_r1: raise HaddockValidationError(“You must supply active and/or passive residues for your first protein.”)’) File “spyder.modules.core::error.py”, line 92, in \_raise exec(statement, lastframe.f\_globals, lastframe.f\_locals) File “”, line 1, in HaddockValidationError: You must supply active and/or passive residues for your first protein. ---
**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:** [April 7, 2017, 7:55am UTC](https://ask.bioexcel.eu/t/selecting-interacting-residue-for-docking/338/8 "2017-04-07T07:55:35Z")
You are doing something wrong… I run yesterday the random patch protocol without problem… Which fields are you exactly filling in? ---
**Author:** ![diffracteD](https://avatars.discourse-cdn.com/v4/letter/d/958977/32.png) [@diffracteD](https://ask.bioexcel.eu/u/diffracteD)\ **Post date:** [April 7, 2017, 8:06am UTC](https://ask.bioexcel.eu/t/selecting-interacting-residue-for-docking/338/9 "2017-04-07T08:06:39Z")
First Molecule: Submitting DNA (PDB) Chain to be used - All Segment ID for docking - A Molecule type - DNA Second Molecule: Submitting ligand (PDB) Chain to be used - All Segment ID - B Molecule type - protein/peptide/ligand Distance Restraints: Define randomly ambiguous interaction restraints from accessible residues - checked Sampling parameters: Number of structures for rigid body docking - 10000 Number of structures for semi-flexible refinement - 400 Number of structures for the explicit solvent refinement - 400 Clustering Parameters: Clustering method - RMSD RMSD cutoff - 2.0 Advanced Sampling: initial temperature for second TAD cooling step with flexible side-chain at the inferface (i think that’s interface) - 500 initial temperature for third TAD cooling step with fully flexible interface - 300 number of MD steps for rigid body high temperature TAD - 0 number of MD steps during first rigid body cooling stage - 0 That’s all I have modified. Please give some comment. ---
**Author:** ![sola\_sola](https://avatars.discourse-cdn.com/v4/letter/s/b5a626/32.png) [@sola\_sola](https://ask.bioexcel.eu/u/sola_sola)\ **Post date:** [October 30, 2018, 6:45am UTC](https://ask.bioexcel.eu/t/selecting-interacting-residue-for-docking/338/10 "2018-10-30T06:45:42Z")
I had the same problem, did you solve it?