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Docking

Executing the clean_pdb.py script

Category: 
Docking

Hello All,

I am currently running RosettaCommons on linux and am attempting to run the clean_pdb.py script on my native protein.
As of now, I have changed it to an executable file as recommended, but I am unsure what the command is to run this script on a certain pdb.

As of now my command is $ python clean_pdb.py script path/to/pdb, but this doesnt appear to be correct. Can anyone direct me on what the script requires for a command and exactly what to type in so it runs it on my vinculin.pdb protein.

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Output structures from docking_prepack_protocol: initial__*.pdb vs prepack__*.pdb, which one should I send to docking_protocol?

Category: 
Docking

docking_prepack_protocol generates several output pdb structures:

away__*_0001.pdb
away_packed__*_0001.pdb
initial__*_0001.pdb
prepack__*_0001.pdb
*_0001.pdb

where * stands for the name of the crystal structure that was given as input to docking_prepack_protocol.

What are the differences between these .pdb files that docking_prepack_protocol outputs?

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Reproduce Robetta's ddg values of interface alanine scan using Rosetta?

Category: 
Docking
Scoring

Is there a protocol on Rosetta to obtain Robetta's (http://robetta.bakerlab.org/) ddg's calculations of interface alanine scan functionality?
I don't care if they use an older version of Rosetta. I just want to obtain ddg's values that are as close as possible to those returned by Robetta. What protocol do they use?

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How to automatically position new peptides into the binding site of a enzime, in order to run peptide-protein docking approaches

Category: 
Docking

Hello,
I would like to know how to automatically position new peptides into the binding site of a enzime, in order to run peptide-protein docking approaches?
In my case, I know the binding site and I have the crystallographic structure of a reference peptide located at the binding site, but I need to generate several (thousands) of other new linear peptide structures at this same binding site, in order to run the docking calculations using the rosetta3 protocols.

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Docking with constraint

Category: 
Docking

Hi everyone,
I am trying to dock a domain into a dimer protein. The domain is lowest score structure that was generated by abinition relax. Because they are continous amino acid sequence, so i use atompair constraint betwen c terminal of first monomer with n terminal of predicted domain. I also constraint its c terminal with n terminal of the second mononer.

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Combine flags file with command line arguments?

Category: 
Compilation
Structure prediction
Docking
Design
Scoring
Enzyme Design
Loop Modeling
Constraints
Symmetry
Small Molecules
Chemically Modified Residues
Fragment Generation
Membrane
Non-Canonical Peptides
Nucleic Acids
Phenix / MR Rosetta

Is it possible to combine a flags file with command line arguments?

For example, something like this:

minimize_with_cst.linuxgccrelease -in:file:l min_pdb_file_list @flags_file

where flags_file contains additional options. Moreover, what is the effect of changing the order of command line arguments and flags files? Which takes precedence? That is, what is the difference between the above command and:

minimize_with_cst.linuxgccrelease @flags_file -in:file:l min_pdb_file_list

Thanks.

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ratio of conformers and docking output

Category: 
Docking

Hi,

I am performing docking claculations using RosettaLigand. I have two questions regarding RosettaLigand docking:

1. How does Rosetta ligand process the ligand conformers fed to dock a structure? I mean does it try all the ligand conformers sequentially in the input file or does it pick them randomly, if so on what criteria?

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