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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.
docking_prepack_protocol generates several output pdb structures:
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?
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?
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.
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.
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
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?