The scripts and input files that accompany this demo can be found in the
demos/protocol_captures directory of the Rosetta weekly releases.
This is a protocol capture, and represents the protocol at a fixed point in time. It may not work with the current version of Rosetta.
KEYWORDS: SURFACES GENERAL
written by Michael Pacella (Graylab), email@example.com
This demo will describe how to run the C++ version of the RosettaSurface algorithm. The test case shown here will analyze the adsorption of the model peptide LK-alpha to the 104 surface of calcite
Simultaneous optimization of protein rigid-body orientation, backbone and side chain conformations on a solid surface.
surface_docking<.exe> -database <path/to/database> @input/flags
Ensure that the input pdb is properly formatted with the protein appearing before the surface in the input file and belonging to a separate chain
Ensure that the specified surface vectors match the input surface
Ensure that parameter files corresponding to the molecules comprising the surface exist in the rosetta database
(in the directory with output decoys)
Make sure that the folder contains either only adsorbed state PDBs (and native.pdb) or solution state PDBs. Also make sure that all post processing scripts (found in the scripts/post_processing directory) are present in this directory as well
These commands will extract the top 4 adsorbed-state decoys for analysis and generate secondary structure, protein-protein contact maps, and protein-surface contact maps
This app requires a single protein positioned above a solid surface whose parameters are present in Rosetta. The protein needs to appear before the surface in the pdb file and the two need to be separate chains