# Run TwoStubs on scaffolds. 

#! /bin/bash

    dhead=`pwd`
for f in $(ls ~/Documents/protein_design_thesis/1CZ8/docking_stubs/7_place_two_stubs/7-baker/5/*/*anti.patchdock.1.pdb); do
    b=`basename $f anti.patchdock.1.pdb`
  
    d=`dirname $f`
    cd $d

    
/home/highbiotech/linux_programs/rosetta_bin_linux_2017.39.59729_bundle/main/source/bin/rosetta_scripts.static.linuxgccrelease -database /home/highbiotech/linux_programs/rosetta_bin_linux_2017.39.59729_bundle/main/database -s $f -parser:protocol ~/Documents/protein_design_thesis/1CZ8/docking_stubs/7_place_two_stubs/7-baker/5/my_two_native_stubs.xml  -ignore_unrecognized_res -out:nstruct 1000  -beta -mute core.util.prof -out:file:fullatom -mute core.io.database -overwrite -use_input_sc -docking:no_filters >$b.log

done

cd $dhead