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Docking

Ligand Docking with RosettaScripts gives a ParsedProtocol exception

Category: 
Docking

I am trying to run a ligand docking simulation, and am running into a few technical limitations. I am trying to follow the tutorial form the Meiler lab (only with a different starting pdb and ligand).

I am running the command:

rosetta_scripts.linuxgccrelease -database $ROSETTA_DATABASE -in:file:s /inputs/4XXX_model.pdb /inputs/MyLigand.pdb -in:file:extra_res_fa /inputs/MyLigand.params -nstruct 3 -parser:protocol /scripts/xml/dock.xml -mistakes:restore_pre_talaris_2013_behavior true

Post Situation: 

can not find a residue type that matches the residue HIS_P:NtermProteinFull

Category: 
Docking

Hi,

I have been trying to dock a protein and peptide at pH 5.5 using pH_mode as described by Kilambi and Gray's protocol. However, if I omit the keep_input_protonation_state flag the SFR builder removes the protons from the protonated residues. If I keep the keep_input_protonation_state flag I get a "can not find a residue type that matches the residue HIS_P" error. Is there a fix for that?

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Docking Prepack protocol working or not ?

Category: 
Docking
Scoring

Hi Rosetta community, 

I'm running the prepack protocol using as input a PDB file containing a dimer (chain A and B). The protocol seemed to work ("... reported success in 3 seconds") but I get the following warning : 

[ WARNING ] When switching to a fa_standard ResidueTypeSet:  Pose already contains fa_standard ResidueTypes.

and my score_sc file contains 0.000 for the total score for every generated structure.

Here the command I used to run prepack:

Post Situation: 

Extremely low interface scores with "local refinement"

Category: 
Docking

Hi,

I am using Rosetta local refinement to calculate the interface scores of known protein complexes (in a bound form).

In the docking protocol, it says "Typical values for I_sc of godd decoys are in the range of -5 to -10.". However, for some complexes, rosetta local refinement gives me I_sc as low as -5988.1. This number doesn't seem realistic to me. Could you please explain why we see such small numbers? How can we interpret this result, if the good binding score is in the range of -5 and -10?

Post Situation: 

Error running snugdock

Category: 
Docking

Hi,

I'm following the antibody modeling protocol recently published in Nature Protocols "Modeling and docking of antibody structures
with Rosetta".  I run into an error when running snugdock with ensembles.  I get a segfault (last couple lines posted) with no additional info.  However, if I don't specify to run with ensembles, the snugdock run proceeds to completion.  I'm using rosetta3.8.

 ~/rosetta/bin/snugdock.linuxgccrelease @snugdock.flags

tail of output:

Post Situation: 

Features Reporters missing documentation in rosetta_scripts -info

Category: 
Docking

Running the command 

rosetta_scripts.macosclangrelease -info InterfaceFeature

with randomly selected Features Reporters always returns an error. The info flag behaves correctly for other Rosetta Scripts tags for example passing MutateResidue. 

Rosetta 3.8 on Mac OSX.

core.init: Rosetta version unknown:exported  from http://www.rosettacommons.org

core.init: command: rosetta_scripts.macosclangrelease -info InterfaceFeature

Post Situation: 

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.]

Post Situation: 

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