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Docking

Bound Ligand Protein-Protein Docking

Category: 
Docking

Hi,

I am trying to run on the Rosie server some docking2 tests with bound ligand in each protein. In fact, I would like to explore a situation of how two protein interacts with each other with bound ligand. However, when I launch jobs with ligand coordinates at its final site included in the PDB, the simulation fails and I receive an error message.

I, therefore, write to ask whether is it possible to do on ROSIE server?

I thank you all in advance,

Haresh

Post Situation: 

ERROR: Specified chain does not exist.

Category: 
Docking

Hello,

I am using already preinstalled software Rosetta 3.10 on ComputeCanada (CCDB). I have run demos tutorial of protein-protein docking, was running successfully. Later, I have submitted own protein-protein docking job. I got an error(see below). Please, I need to help solve this problem.

 

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[ajanihar@gra-login3 input_files]$ rosetta_scripts.mpi.linuxiccrelease @docking_full.options -parser:protocol docking_full.xml -out:suffix _full -nstruct 5

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Segmentation Fault

Category: 
Docking

Hi,

I am trying to use protein-protein docking with unbound ligand protein and, I still get this error(see below ). I would appreciate any suggestion or solution.

Looking forward to hearing from you.

Haresh 

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Does Snugdock remodeling of H3 loops include the kink constraint as in RosettaAntibody?

Category: 
Structure prediction
Docking

I am docking an antibody that has 20 residues in the H3 loop.  I realize that this is a very challenging case.  From the 2017 paper by Weitzner and Gray, I understand the importance of a kink constraint in H3 loop modeling.  I want to know if the H3 loop remodeling that occurs during snugdock includes the kink constraint.  If not, I am concerned that the kink will be lost during remodeling, especially for this long loop.

 

 

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help surface_docking peptide on ice

Category: 
Docking

Hello everyone,

I am trying to use Rosetta surface_docking protocol to dock a 12 residues peptide on an ice slab.

I tried different formatting options of the input ice - peptide PDB file, but the software crashes.

After looking at the existing (Unsolved) posts on the forum, I created a PDB file formatted in this way:

Post Situation: 

Docking to TM protein plus lipid bilayer

Category: 
Docking

Hi, I want to dock a protein to a TM protein embedded in a lipid bilayer.

Is there a way to do that with an implicit membrane model?

My current approach is to place explicit POPC lipids around the TM protein. 

What would be the simplest way to make Rosetta being able to read the pdb file containing POPC?

Thanks!

Post Situation: 

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: 

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