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Docking

Protein Protein Docking with bound ligands

Category: 
Docking

Hi There,

Myself Haresh, I am postdoctoral fellow at University of Toronto. I used PyRosetta for protein protein docking and working good. Usually rosetta did protein protein doking between only two proteins. Is there any avaiblity or options to do protein-protein docking with bound ligand with each protein(e.g. Protein-Ligand --- Ligand-Protein)? Thanks in advance for your help.

Looking forward to hear from you.  

Post Situation: 

protein ligand docking

Category: 
Docking

Hello!

I'm not able to generate a score.sc file because something is not allowing me to dock my ligands to my protein.  I get the error

 Cannot normalize xyzVector of length() zero
Error: [ ERROR ] 
Error: [ ERROR ] Treating failure as bad input; canceling similar jobs

Here's an example of my params file.  I've attached a copy of my ligand/receptor .pdb and my dock.xml as well:

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Pyrosetta doesn't recognize the correct docking partners

Category: 
Docking

Hi all,

I can run rosetta docking protocol on my pdb file and there is no problem when I define partners as "MN_A". However, the same doesn't work on pyrosetta demo code of docking. I tried to solve this in several different ways by changing the docking jump value or etc but nothing acheived! Output models are still wrong in the format of M_NA. How can I fix this?

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Regarding snugdock Ag-Ab score

Category: 
Docking

Hi There,

I am running snugdock locally for an Ag-Ab complex.  Program is running fine but I am getting all score value 0.00.

SCORE: total_score         rms CAPRI_rank       Fnat       I_sc       Irms   Irms_leg atom_pair_constraint                cbeta              cen_rms chainbreak complex_normalized           dG_cross dG_cross/dSASAx100 dG_separated dG_separated/dSASAx100 dSASA_hphobic dSASA

Post Situation: 

docking parse error

Category: 
Docking

Hello,

I'm trying to use the highres docking protocol  with rosetta3.9 and I still get this error (see below), no matter what I do with the xml protocol (attached):

I would appreciate any suggestion
best regards,
Dave

The command I run:
rosetta_scripts.static.linuxgccrelease -in:file::s 1mj5.pdb -parser:protocol docking.xml -extra_res_fa r_lig.params

 

Post Situation: 

docking with capping groups

Category: 
Docking

Hi,

I am trying to dock a peptide into a protein with rosetta. My peptide and protein have capping groups (ACE, NMA), which are recognized by the relax protocol and incorporated into the terminal residues. I then put the relaxed structures together into a complex.pdb file and tried to run the docking protocol:

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DockingProtocol mover ensemble error

Category: 
Docking

Hi all,

I would like to know if the mover DockingProtocol allows the use of ensemble for running docking with RosettaScripts.

I have an ensemble for both protein partners and I have used the flags -ensemble1 and -ensemble2.

If I use the DockingProtocol mover (script file test1.xml attached) aparently it does not turn ON the ensemble flag and I get an unexplained error:

 

...

Post Situation: 

Negative Design

Category: 
Docking

Hello,

 

I am trying to come up with a protocol (xml script) that will allow me to perform positive design for one substrate and negative design for the inhibitor. Our goal is to create a protein that maintains functionality and is resistant to the inhibitor.

I am open to any suggestion. I have not been able to find any documentation on how to perform docking_design in this manner.

Thanks

Post Situation: 

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