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Docking

General question regarding ligand-docking

Category: 
Docking

I am quite new to Rosetta. I have a very simple questions regarding general concepts about ligand-docking. I am a little bit confused about how to set parameter to ensure that all conformers generated can be tested. Lets say if I have a PDB containing 50 conformers. If I set -nstruct = 1 and run docking.xml with transformer like this (Transform name="predock" chain="X" box_size="20" move_distance="2" angle="20" cycles=“500” repeats=“2” temperature=“5”/>). What does really happen through the docking simulation? 

 

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ligand docking error

Category: 
Docking

Dear all:

I am a beginner of Rosetta. While I am running ligand-docking toturial (https://www.rosettacommons.org/demos/latest/tutorials/ligand_docking/ligand_docking_tutorial). I encounter an error when run script calculate_ligand_rmsd.py when doing data analysis. This script is used to calculate RMSD of each model comapred with the best model. When I run this script, the error indicated :

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DNA-protein docking

Category: 
Docking
Nucleic Acids

I didn't find any contemporary comment on that so I'd like to ask about how to dock protein structure to dsDNA in Rosetta? Is that possible now anyhow?

I have small protein structural motif, like HTH and try to model its interaction with a sequence within dsDNA to get some hints about which residues will bind to which DNA bases so I don't have to scan along huge DNA strands but rather have a well-defined location within the major groove to explore.

Thanks for all advice.

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my status jobs been queued in such longer time

Category: 
Docking

Hi there,

I saw most status of daemon showed [DEAD]. I had sent multiple jobs using peptiderive methods. However, till now my jobs still in queue listing. What happened actually in there? stuck?. Please response this email as soon as possible. I need these data info to make up my article. Here in my list of jobs:

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Docking of multichain oligomers

Category: 
Docking

Hi all,

I'm trying to perform docking simulations for two identical coiled-coil homodimers modelled by the fold and dock protocol to establish the potential ways of interaction of these in higher order complexes (there's an experimental evidence for the formation of such assemblies).

 

The command looks as follows:

docking_protocol.linuxgccrelease -in:file:s S_029104.pdb -unboundrot S_029104.pdb -nstruct 1  -randomize1 -randomize2 -ex1 -ex2aro -partners AB_AB 

 

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antibody_numbering_converter cannot recognize the IMGT scheme

Category: 
Docking

To whom it may concern:

Hi I want to convert my antibody structure from Chothia to IMGT. I use the following command and get an error "ERROR: Illegal value specified for option -antibody:output_ab_scheme : IMGT". I am wondering is the IMGT scheme already cancelled in the number converter program? This is a 2019.35.60890 version.

/home/rosetta_bin_linux_2019.35.60890_bundle/main/source/bin/antibody_numbering_converter.linuxgccrelease -input_ab_scheme Chothia -output_ab_scheme IMGT -s 1ahw_chothia.pdb

 

Best regards,

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Error in src/protocols/membrane/util.cc line: 1224

Category: 
Docking

Hi, I am trying to prepare a MPDocking run (v 2019.35).

Both prepacking as well as actual docking crash with the same message:

ERROR: The SpanningTopology object in MembraneInfo is empty!
ERROR:: Exit from: src/protocols/membrane/util.cc line: 1224

However, the attached log file seems to indicate that the molecule was read correctly. Also the TMspans were build and their center calculated (end of logfile).

 

 

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