Performing Protein-Protein Docking in Haddock


#1

Hi, I wish to perform protein-protein docking in Haddock. However, I have no information about the active residues for both the receptor protein and the ligand protein. I tried checking the option “Define randomly ambiguous interaction restraints from accessible residues” and I didn’t define any active/passive residues. But it returned with an error claiming that I have at least define active/passive residues for the 1st molecule.

What should I do to resolve this problem? Thank you.


#2

You must be accessing the expert interface in that case. Make sure not to define any active and passive residues for the molecules.

Then indeed turn on the “Define randomly ambiguous interaction restraints from accessible residues”

You will also need to sample more (e.g. 10000/400/400 models for it0, it1 and water


#3

Thanks for the confirmation. I tried it and I got the following error message:

There was an error in the authorisation routine of the server

Full error information:

Traceback (most recent call last):
File “/home/enmr/services-enmr/HADDOCK2.2/py/haddockserver.py”, line 305, in serve_haddock
dd2 = newmodel.convert(auth).convert(HaddockGuruInterface).convert(HaddockMultiRunParameters)
File “haddock::HaddockExpertInterface.spy”, line 1270, in convert
c = spyder.core.convert(HaddockExpertInterface, 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 174, in execute_path
result = execute_path(c.outtype, arg, pathtail, failed, visited, method,splitcounter,methodindex)
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.

Does that mean I have no authorisation to use the Expert interface? >.<


#4

Exactly. But you can request elevated access on your registration page.