Selecting interacting residue for docking

HADDOCK
1

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.

2

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

3

Thank you for the tutorial link.
Yes. The ligand is newly synthesized. That’s why I’m trying the Prediction mode in the webserver.

4

PS: You don’t need the prediction interface for this. Rather follow the tutorial I would say

5

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.

6

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.

7

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.typesc.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.

8

You are doing something wrong… I run yesterday the random patch protocol without problem…
Which fields are you exactly filling in?

9

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.

10

I had the same problem, did you solve it?