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Docking

Ensemble docking causes segmentation fault 11

Category: 
Docking

Trying to locally dock two ensembles.

Docking runs fine with ensemble lists removed, but adding ensemble lists causes segmentation fault 11 on both mpi linux (Stampede) and MacOS. 

At output level 400 on Mac, it looks like the crash comes during the first cycle of low-res docking:

Suggestions?

 

protocols.docking.DockingLowRes: 

protocols.docking.DockingLowRes: ////////////////////////////////////////////////////////////////////////////////

Post Situation: 

Rosetta Antibody Prepack - Problem HL_A vs. LH_A

Category: 
Docking

Dear Rosetta Users,

I am having a problem with the antibody_prepack_protocol, I am again following the Nature Protocols article “Modeling and docking of antibody structures with Rosetta” (doi:10.1038/nprot.2016.180).

Short Story:

I get the following error when I run the prepacking protocol on my antibody, but only when I switch the heavy and light chains from HL to LH:

ERROR: (end_res_ - start_res_ + 1) == conf_size_

Long Story:

Post Situation: 

Error of non standard amino acid (SnugDock)

Category: 
Docking

Hi

I am trying to do a docking with an antibody molecule and its partner protein. As far as I can see, the amino acid residues are perfectly fine. Yet when I try submitting it, I am getting an error about non-standard AA. Please find attached the screenshot of the error message.
Kindly help me get through this problem.

Thanks

Suchetana

 

I am also attaching the input file (though this is not the complete file. I am unable to upload the complete file for size issues. Please suggest a workaround)

Post Situation: 

docking2: will the real prepacked PDB stand up?

Category: 
Docking

In the prepack folder after a successful docking2 run, I have three PDB files:

proteins_prepacked.pdb

proteins.pdb

proteins.prepack.pdb

Why? Which one is the prepacked structure? And, why is prepack_score.sf empty?

SEQUENCE: 
SCORE: total_score description 
SCORE:       0.000 proteins_0001

[All output files attached.]

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Docking prepack vs. relax

Category: 
Docking

Is Docking Prepack simply a specialized version of Relax for dealing with complexes? (separate complex, minimize sidechains, reassemble)

If I am docking proteins A and B where each has already been individually relaxed, is there any need for running Docking Prepack on the PDB file that contains both relaxed A and B, already oriented correctly for local docking?

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Docking membrane ions and water

Category: 
Docking

I'll explain what I do, in case someone has a solution to my problem.
I am trying to perform a docking protein-protein, where, a membrane protein arranged in a lipid membrane and balanced with water and ions, should be bound to a protein.
I need to know how much these structures interfere with docking.


Any tips?

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Error with non-canonical amino acid in SnugDock.

Category: 
Docking

Hi all,

I'm trying to model the binding of an antibody to a citrullinated peptide. I've created rotlibs and params files for the citrulline amino acid following the protocol in Renfrew, et al. "Incorporation of Noncanonical Amino Acids into Rosetta and Use in Computational Protein-Peptide Interface Design", doi:10.1371/journal.pone.0032637. Now I'm trying to use SnugDock to model the antibody:antigen binding, but I keep hitting the following error. 

Post Situation: 

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