OneScience-Group/flex_ddG_tutorial

1Backrub step command line example:
2
3rosetta_scripts.linuxgccrelease
4-parser:protocol flex_ddG-backrub_step.xml
5-s wt_pdb_path # Starting WT crystal structure
6-in:file:fullatom
7-parser:script_vars
8mutate_resfile_relpath=%s # Path to a resfile specifying mutant positions. Can be any set of mutations (only the positions matter), as mutations are made in the next step. Positions need to be known now to pick backrub region.
9backrub_kt=1.2
10backrub_trials=36000
11backrub_stride=12000
12neighbor_distance=12.0
13sc_sample_rotwells_unif=0
14min_tolerance=0.000001
15min_max_iter=5000
16min_abs_score_convergence_threshold=1.0
17
18Mutation step command line example:
19
20rosetta_scripts.linuxgccrelease
21-parser:protocol flex_ddG-mutation_step.xml
22-s wt_minimized_pdb_path # Path to the WT minimized PDB structure from the first script, needed to score ddG calculation
23-native # Path to the starting WT crystal structure, needed so that same neighbor residue bubble is selected
24-in:file:fullatom
25-parser:script_vars
26chainstomove=%s
27mutate_resfile_relpath=%s # Path to resfile specifying mutations
28min_tolerance=0.000001
29min_max_iter=5000
30neighbor_distance=12.0
31min_abs_score_convergence_threshold=1.0
32backrub_pdb_path=%s # Path to backrub PDB output from earlier step, mutations will be applied to this model