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i'm trying to dock a peptide into kinase. It's very important to keep ATP molecule in the kinase ortherwise some peptide simulation model will occupy ATP's position.
But the flexpepdock will remove all not aminoacid molecules. I was wondering is there any way I can do that ? Or an alternative module on Rosetta?
I had to reinstall newest rosetta (rosetta_bin_linux_2017.39.59729_bundle), but after successful installation and compilation, when I want to get docking using following commands and script:;
~/linux_programs/rosetta_bin_linux_2017.39.59729_bundle/main/source/bin/rosetta_scripts.default.linuxgccrelease -database ~/linux_programs/rosetta_bin_linux_2017.39.59729_bundle/main/database/ -nstruct 200 -s 1czH_1czW.pdb -ex1 -ex2 -parser:protocol docking_stubs.xml
I am new to using Rosetta. I would like to make a res file to mutate through all 20 amino acids in a Protein-protein interface and predict binding energy using RosettaDesign. This might be a stupid question but how to you make a resfile? Do you write it in text edit? Is the file extention .res?
I have found the refile syntax page from Rosettas website but it does not say where you type any of the commands into or how to save it.
I follow the ligand docking tutorial from here: https://www.rosettacommons.org/demos/latest/tutorials/ligand_docking/ligand_docking_tutorial
When I get to point 6 and try to run docking protocol via ./rosetta_scripts.linuxgccrelease @options it says ERROR: Cannot open file "3PBL_ETQ.pdb"
How can I check the particular path to the file and correct, if needed?
Thanks in advance!
I have two domains that are asymmetric and I want to dock them using topology broker (asymmetric fold and dock like operation). Below is the full description of my problem:
1. I have pdbs for two domains that I want to dock. Domain1 has 3 chains and domain2 and 1 chain