Protein-RNA to RNA Docking

Hi,
I would like to perform docking of an RNA-protein complex (input 1) to an RNA (input 2). The complex forms 3 bp to my RNA, which I provided as tbl file (Hydrogen bond restraints). I defined the other contacts (protein to RNA) as “active residues”, but the docking results never formed base pairs and the active residues are not even close to each other.
How can I provide more information about the active residues or specialize the contacts?

Thank you so much for your help.

Vanessa

I would carefully check your distance restraints.

Look also at a output file from the rigid body stage (it0) and search for NOE.
Check if your restraints are properly read - it could be there is a problem in the way you defined those and they are not used…

With distance restraints you mean the tbl file?
Thank you

Yes - check carefully the syntax

This is my tbl file:

assign ( segid A and resid 1510 and name N3 )( segid B and resid 110 and name N1 ) 2.91 0.5 0.5
assign ( segid A and resid 1510 and name N3 )( segid B and resid 110 and name H1 ) 1.89 0.5 0.5
assign ( segid A and resid 1510 and name N4 )( segid B and resid 110 and name O6 ) 2.72 0.5 0.5
assign ( segid A and resid 1510 and name O2 )( segid B and resid 110 and name N2 ) 3.08 0.5 0.5
assign ( segid A and resid 1510 and name H42 )( segid B and resid 110 and name O6 ) 1.71 0.5 0.5
assign ( segid A and resid 1510 and name O2 )( segid B and resid 110 and name H22 ) 2.08 0.5 0.5
assign ( segid A and resid 1508 and name N3 )( segid B and resid 112 and name N1 ) 2.91 0.5 0.5
assign ( segid A and resid 1508 and name N3 )( segid B and resid 112 and name H1 ) 1.89 0.5 0.5
assign ( segid A and resid 1508 and name N4 )( segid B and resid 112 and name O6 ) 2.72 0.5 0.5
assign ( segid A and resid 1508 and name O2 )( segid B and resid 112 and name N2 ) 3.08 0.5 0.5
assign ( segid A and resid 1508 and name H42 )( segid B and resid 112 and name O6 ) 1.71 0.5 0.5
assign ( segid A and resid 1508 and name O2 )( segid B and resid 112 and name H22 ) 2.08 0.5 0.5
assign ( segid A and resid 1509 and name N1 )( segid B and resid 111 and name H3 ) 1.93 0.5 0.5
assign ( segid A and resid 1509 and name N1 )( segid B and resid 111 and name N3 ) 2.95 0.5 0.5
assign ( segid A and resid 1509 and name N6 )( segid B and resid 111 and name O4 ) 2.83 0.5 0.5
assign ( segid A and resid 1509 and name H62 )( segid B and resid 111 and name O4 ) 1.82 0.5 0.5

It looks reasonable to me.

Did you search for ERR in an output file?

We can take a quick look if you share the link to your run

thank you so much!

Whoa! This is a huge and complex system.

You should define your H-Bond distance restraints in the unambiguous class and not give them as hbonds as those are only used in it1/final refinement.
Those were more meant to maintain the secondary structure for example.

Or if you still want to define them as hbond restraints, then in the docking parameter:

- unfold the restraint energy constant menu
- in the energy constant for hydrogen bond menu set the first iteration to it0

Conformational changes might also play a role here and we are limited in what we can do.
You could define fully flexible segments for the RNA region supposed to hydrogen bond.

Also to simplify and speed up the computations consider removing any unneeded parts…