cleanUrl: "rosetta-cartesian-ddg-usage"
description: "Rosetta cartesian_ddg의 사용법을 정리합니다."
Rasp이 학습한 target value라고 함.
First, input pdb should be properly relaxed in cartesian space with unrestrained backbone and sidechain coordinates.
This is the command line we used for preminimization:
$ROSETTABIN/relax.static.linuxgccrelease -s $pdb -use_input_sc \\
-ignore_unrecognized_res \\
-nstruct 20 \\
-relax:cartesian-score:weights ref2015_cart \\
-relax:min_type lbfgs_armijo_nonmonotone \\
-relax:script cart2.script \\
-fa_max_dis 9.0 # modify fa_atr and fa_sol behavior, really important for protein stability (default: 6). This flag needs to match what is used in the cartesian ddg options below.
with file "cart2.script":
switch:cartesian
repeat 2
ramp_repack_min 0.02 0.01 1.0 50
ramp_repack_min 0.250 0.01 0.5 50
ramp_repack_min 0.550 0.01 0.0 100
ramp_repack_min 1 0.00001 0.0 200
accept_to_best
endrepeat
$ROSETTABIN/cartesian_ddg.static.linuxgccrelease
-database $ROSETTADB
-s [inputpdb]
-ddg:mut_file [mutfile] # same syntax with what being used in ddg-monomer application.
-ddg:iterations 3 # can be flexible; 3 is fast and reasonable
-force_iterations false (default True) #If this flag is on the protocol will stop when the results converge on a score
-ddg::score_cutoff 1.0 #If the lowest energy scores are within this cutoff the protocol will end early.
-ddg::cartesian
-ddg::dump_pdbs false # you can save mutants pdb if you want
-bbnbr 1 # bb dof, suggestion: i-1, i, i+1
-fa_max_dis 9.0 # modify fa_atr and fa_sol behavior, really important for protein stability (default: 6)
-[scorefunction option]: any other options for score function containing cart_bonded term, for example, -beta_cart or
-score:weights talaris2014_cart]
-ddg::legacy false #Using the latest version of the code
For ddg:mut_file format, please refer to here . Note that this file contains the mutations you want to introduce at once, which means, specifying more than one mutation in a single file will try to mutate all together at same time. Scanning over separate mutations (e.g. ALA scanning) will therefore require running this app separately using different mut_file as input.
relax.static.linuxgccrelease \\
-in:file:s XXXXX.pdb \\
-relax:constrain_relax_to_start_coords \\
-out:suffix _relaxed \\
-out:no_nstruct_label \\
-relax:ramp_constraints false