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Rasp이 학습한 target value라고 함.
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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 $pdb -use_input_sc \
-ignore_unrecognized_res \
-nstruct 20 \
-relax:cartesian-score:weights ref2015_cart \
-relax:min_type lbfgs_armijo_nonmonotone \
-relax:script cart2.script \
-fa_max_dis 9.0 # modify fa_atr and fa_sol behavior, really important for protein stability (default: 6). This flag needs to match what is used in the cartesian ddg options below.
with file "cart2.script":
switch:cartesian
repeat 2
ramp_repack_min 0.02 0.01 1.0 50
ramp_repack_min 0.250 0.01 0.5 50
ramp_repack_min 0.550 0.01 0.0 100
ramp_repack_min 1 0.00001 0.0 200
accept_to_best
endrepeat
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$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
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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.
ThermoNet 이 사용한 relax 코드
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
Shell
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