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Docking

Rigid body perturbation while docking

Category: 
Docking

ERROR: NAN occurred in H-bonding calculations!
ERROR:: Exit from: core/scoring/hbonds/hbonds_geom.cc line: 1122
Traceback (most recent call last):
  File "docking.py", line 118, in <module>
    jobs, job_output)
  File "docking.py", line 79, in sample_docking
    perturb.apply(test_pose)    
RuntimeError: unidentifiable C++ exception

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Fixing part of a ligand in dock-design

Category: 
Docking
Design

Hi,

 

I am using a dock-design protocol to design a binding pocket to bind a ligand. I know where parts of the ligand should bind (orinetations and the position in protein) but the other parts can be flexible. Right now after the dock and design protocol, most of my outcomes change the whole position of ligand and don't keep that part fixed. Is there a way to tell the program to keep parts of the ligand fixed? or a way to generate conformers for only parts of the ligand? 

 

Thanks.

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Docking seems to not parse the -nstruct flag

Category: 
Docking

Hello all,

I am new to Rosetta, and I am trying to get RosettaDock to work.

For the sake of simplicity, I just want to do a refinement dock, with no constraints (though I will eventually want to graduate to incorporating these).

The command I run, a modification on the example commands in Chaudhury et al. 2011:
(I did prepacking before this, with seemingly no issue.
Also, I removed the -database flag, it was causing errors and Rosetta programs seems to work without it.)

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RosettaLigand: How to score native pose in protein-ligand docking experiment?

Category: 
Docking

Hi Everyone:
I'm working on protein-ligand docking experiment. I have an odd problem concerning how to calculate the "native pose" total_score , interface_delta and ligand_auto_rms_no_super value from rosettaligand docking experiment.

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What is "repack", "prepack"?

Category: 
Structure prediction
Docking
Design

All over the place in Rosetta Documentation, I find the terms "repack", "prepack". But I have not found their definitions. I suspect that "repack" and "prepack" refer to conformational samplings where only amino acid side chains are moved, while the backbone remains fixed, but I can't be sure. Is it in this sense that these terms are used here?

What are the definitions of "repack" and "prepack" (in the common usage of these terms in the ROSETTA community)?

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Jump::random_trans strange behavior

Category: 
Docking

Hi to everyone!

I have a complex: protein and peptide (AB chains). I need to make small random shifts of peptide. I do it so

numeric::Real step_size(1.0);
core::kinematics::Jump flexible_jump = pose.jump(pose.num_jump());
flexible_jump.random_trans(step_size);
pose.set_jump( pose.num_jump(), flexible_jump );

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what does initialize_rigid_body_dofs do?

Category: 
Docking

I am doing SymDock using Rosetta 3.5. I wonder what the option really does:

-symmetry:initialize_rigid_body_dofs - Initialize the rigid body configuration according to the symmetry definition file.

I actually ran SymDock using diff. option combinations. When initialize_rigid_body_dofs is set, the assemblies look very different, otherwise more homogeneous. So I concluded that the option does initialization.

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