SetSeed InfilePrefix // Note: the training atoms are needed for patching up chain breaks // when reading in conformations. InFilePrefix /projects/compbio/experiments/undertaker/atoms-inputs/ ReadTrainingAtoms dunbrack-40pc-3157.atoms # The rotamer library need not be from the same set of chains as the TrainingAtoms. # It encodes the most probable conformations of sidechain and backbone # for each residue type. ReadRotamerLibrary dunbrack-40pc-3157.rot Time //Need to read in target before specific fragments or alignments can // be read, also before constraints can be defined. InFilePrefix # ReadTargetPDB T0397.blank.pdb ReadTargetSeq T0397.a2m 1 NameTarget T0397 PopConform InFilePrefix include costfcn-init.under # include MQA_init.costfcn include try10.costfcn // Scale the break and clashe costs down, then gradually back up again ScaleCost break 0.25 soft_clashes 0.04 Time MakeGenericFragmentLibrary Time OutFilePrefix decoys/ InFilePrefix ReadTemplateAtoms Template.atoms // Edit this to include full sets of alignments from any // strongly-predicted superfamily // For M1-K82 InfilePrefix 1jicA/ include read-alignments-scwrl.under InfilePrefix 2fb7A/ include read-alignments-scwrl.under InfilePrefix M1-K82/1jicA/ include read-alignments-scwrl.under InfilePrefix M1-K82/2fb7A/ include read-alignments-scwrl.under // For G80-E150 InfilePrefix 3crkC/ include read-alignments-scwrl.under InfilePrefix 2evbA/ include read-alignments-scwrl.under InfilePrefix G80-E150/3crkC/ include read-alignments-scwrl.under InfilePrefix G80-E150/2evbA/ include read-alignments-scwrl.under # TryAllAlign shrink 0 min_keep_length 1 # NameConform T0397.try10-al1 Include T0397.t04.undertaker-align.under Include T0397.t06.undertaker-align.under # TryAllAlign shrink 0 min_keep_length 1 # NameConform T0397.try10-al1A // For M1-K82 InfilePrefix 2eheA/ include read-alignments-scwrl.under InfilePrefix 2q41A/ include read-alignments-scwrl.under InfilePrefix 2q0dA/ include read-alignments-scwrl.under InfilePrefix 2pt6A/ include read-alignments-scwrl.under InfilePrefix 2pwpA/ include read-alignments-scwrl.under InfilePrefix 1y96A/ include read-alignments-scwrl.under InfilePrefix M1-K82/2eheA/ include read-alignments-scwrl.under InfilePrefix M1-K82/2q41A/ include read-alignments-scwrl.under InfilePrefix M1-K82/2q0dA/ include read-alignments-scwrl.under InfilePrefix M1-K82/2pt6A/ include read-alignments-scwrl.under InfilePrefix M1-K82/2pwpA/ include read-alignments-scwrl.under InfilePrefix M1-K82/1y96A/ include read-alignments-scwrl.under // For G80-E150 InfilePrefix 3bg3A/ include read-alignments-scwrl.under InfilePrefix 3bg5A/ include read-alignments-scwrl.under InfilePrefix 1y8oB/ include read-alignments-scwrl.under InfilePrefix 1hpcA/ include read-alignments-scwrl.under InfilePrefix 1bdoA/ include read-alignments-scwrl.under InfilePrefix 1zkoA/ include read-alignments-scwrl.under InfilePrefix G80-E150/3bg3A/ include read-alignments-scwrl.under InfilePrefix G80-E150/3bg5A/ include read-alignments-scwrl.under InfilePrefix G80-E150/1y8oB/ include read-alignments-scwrl.under InfilePrefix G80-E150/1hpcA/ include read-alignments-scwrl.under InfilePrefix G80-E150/1bdoA/ include read-alignments-scwrl.under InfilePrefix G80-E150/1zkoA/ include read-alignments-scwrl.under InFilePrefix # TryAllAlign shrink 0 min_keep_length 1 # NameConform T0397.try10-al2 Include T0397.t2k.undertaker-align.under Include T0397.undertaker-align.under # ReadFragmentAlignment NOFILTER SCWRL force_alignment all-align.a2m # If disulfides are expected to be important, read the aligment # without SCWRL, since it destroys disulfides. # Also SCWRL is *very* slow, so try to use it less on the server. # ReadFragmentAlignment NOFILTER force_alignment all-align.a2m InfilePrefix Time # ReportCost try10.rdb # TryAllAlign shrink 0. min_keep_length 1 # NameConform T0397.try10-al3 # TryAllAlign shrink 0.2 min_keep_length 1 # NameConform T0397.try10-al4 # TryAllAlign shrink 0.3 min_keep_length 1 cumulative # NameConform T0397.try10-al5 # TryAllAlign shrink 0.4 min_keep_length 1 # NameConform T0397.try10-al6 # TryAllAlign shrink 0.5 min_keep_length 1 cumulative # NameConform T0397.try10-al7 # TryAllAlign shrink 0. min_keep_length 1 # NameConform T0397.try10-al8 # SCWRLConform # NameConform T0397.try10 # OutFilePrefix decoys/ # PrintConformPDB T0397.try10-init.pdb // Switch to the following (commenting out the TryAllAlign) // to polish existing models InfilePrefix decoys/ # include read-pdb.under ReadConformPDB T0397.MQAC1-opt1-scwrl.pdb ReadConformPDB T0397.MQAC1-opt1.pdb ReadConformPDB T0397.MQAC1-opt2.pdb ReadConformPDB T0397.MQAC1-opt3.pdb ReadConformPDB T0397.MQAU1-opt1-scwrl.pdb ReadConformPDB T0397.MQAU1-opt1.pdb ReadConformPDB T0397.MQAU1-opt2.pdb ReadConformPDB T0397.MQAU1-opt3.pdb ReadConformPDB T0397.try1-init.pdb.gz ReadConformPDB T0397.try1-opt1-scwrl.pdb.gz ReadConformPDB T0397.try1-opt1.pdb.gz ReadConformPDB T0397.try1-opt2.pdb.gz ReadConformPDB T0397.try1-opt3.gromacs0.pdb.gz ReadConformPDB T0397.try1-opt3.gromacs0.repack-nonPC.pdb.gz ReadConformPDB T0397.try1-opt3.pdb.gz ReadConformPDB T0397.try1-opt3.repack-nonPC.pdb.gz ReadConformPDB T0397.try2-init.pdb.gz ReadConformPDB T0397.try2-opt1-scwrl.pdb.gz ReadConformPDB T0397.try2-opt1.pdb.gz ReadConformPDB T0397.try2-opt2.pdb.gz ReadConformPDB T0397.try2-opt3.gromacs0.pdb.gz ReadConformPDB T0397.try2-opt3.gromacs0.repack-nonPC.pdb.gz ReadConformPDB T0397.try2-opt3.pdb.gz ReadConformPDB T0397.try2-opt3.repack-nonPC.pdb.gz ReadConformPDB T0397.try3-init.pdb.gz ReadConformPDB T0397.try3-opt1-scwrl.pdb.gz ReadConformPDB T0397.try3-opt1.pdb.gz ReadConformPDB T0397.try3-opt2.pdb.gz ReadConformPDB T0397.try3-opt3.gromacs0.pdb.gz ReadConformPDB T0397.try3-opt3.gromacs0.repack-nonPC.pdb.gz ReadConformPDB T0397.try3-opt3.pdb.gz ReadConformPDB T0397.try3-opt3.repack-nonPC.pdb.gz ReadConformPDB T0397.try4-init.pdb.gz ReadConformPDB T0397.try4-opt1-scwrl.pdb.gz ReadConformPDB T0397.try4-opt1.pdb.gz ReadConformPDB T0397.try4-opt2.pdb.gz ReadConformPDB T0397.try4-opt3.gromacs0.pdb.gz ReadConformPDB T0397.try4-opt3.gromacs0.repack-nonPC.pdb.gz ReadConformPDB T0397.try4-opt3.pdb.gz ReadConformPDB T0397.try4-opt3.repack-nonPC.pdb.gz ReadConformPDB T0397.try6-opt1-scwrl.pdb.gz ReadConformPDB T0397.try6-opt1.pdb.gz ReadConformPDB T0397.try6-opt2.pdb.gz ReadConformPDB T0397.try6-opt3.gromacs0.pdb.gz ReadConformPDB T0397.try6-opt3.gromacs0.repack-nonPC.pdb.gz ReadConformPDB T0397.try6-opt3.pdb.gz ReadConformPDB T0397.try6-opt3.repack-nonPC.pdb.gz ReadConformPDB T0397.try7-opt1-scwrl.pdb.gz ReadConformPDB T0397.try7-opt1.pdb.gz ReadConformPDB T0397.try7-opt2.pdb.gz ReadConformPDB T0397.try7-opt3.gromacs0.pdb.gz ReadConformPDB T0397.try7-opt3.gromacs0.repack-nonPC.pdb.gz ReadConformPDB T0397.try7-opt3.pdb.gz ReadConformPDB T0397.try7-opt3.repack-nonPC.pdb.gz ReadConformPDB T0397.try8-opt1-scwrl.pdb.gz ReadConformPDB T0397.try8-opt1.pdb.gz ReadConformPDB T0397.try8-opt2.pdb.gz ReadConformPDB T0397.try8-opt3.gromacs0.pdb.gz ReadConformPDB T0397.try8-opt3.gromacs0.repack-nonPC.pdb.gz ReadConformPDB T0397.try8-opt3.pdb.gz ReadConformPDB T0397.try8-opt3.repack-nonPC.pdb.gz ReadConformPDB chimera-5-6.pdb.gz ReadConformPDB chimeraB-5-6.pdb.gz ReadConformPDB exploded-try5.pdb.gz ReadConformPDB exploded-try6-more.pdb.gz ReadConformPDB exploded-try6.pdb.gz CostConform Time // The following alignments are not as good as the ones tried above, // so are not used in getting the starting point. InFilePrefix ReadFragmentAlignment fragment_only T0397.t2k.many.frag ReadFragmentAlignment fragment_only T0397.t04.many.frag ReadFragmentAlignment fragment_only T0397.t06.many.frag // The next 3 lines save the templates in a single file, to avoid having // to reread the PDB files. Note that ReadTemplateAtoms should be called // before any ReadFragmentAlignments to take full advantage of this // cached results. OutFilePrefix # PrintTemplateAtoms Template.atoms OutFilePrefix decoys/ Time InitMethodProbs \ Backrub 0.5 \ BigBackrub 0.3 \ FixOmega 0.3 \ HealPeptide 0.3 \ JiggleSubtree 0.3 \ JiggleSegment 0.3 \ OptSubtree 0.3 \ OptSegment 0.3 \ OptAllSegments 0.3 \ ShiftSubtree 0.3 \ ShiftSegment 0.3 \ TweakPhiSubtree 0.3 \ TweakPhiSegment 0.3 \ TweakPsiSubtree 0.3 \ TweakPsiSegment 0.3 \ TweakPsiPhiSubtree 0.3 \ TweakPsiPhiSegment 0.3 \ TweakHbondSubtree 0.3 \ TweakHbondSegment 0.3 \ TweakMultimer 0.3 \ TweakPeptide 0.3 \ OneRotamer 1 \ ClashingRotamer 1 \ ClusteredRotamer 2 \ ReduceBreak 5 \ CloseGap 15 \ HealGap 5 \ MoveGap 15 \ ReduceConstraint 10 \ ImproveSSBond 0 \ InsertSSBond 0 \ InsertAlignment 1 \ InsertSpecificFragment 5 \ InsertFragment 5 \ TwoFragment 5 \ CrossOver 5 \ CrossAndInsert 5 \ ReduceClash 5 OptConform pool_size 20 num_gen 60 gen_size 100 \ super_iter 1 super_num_gen 100 \ scwrl_each use_all keep_all NameConform T0397.try10-opt1 PrintConformPDB T0397.try10-opt1.pdb SCWRLConform NameConform T0397.try10-opt1-scwrl PrintConformPDB T0397.try10-opt1-scwrl.pdb CostConform Time ScaleCost break 2 soft_clashes 5 CostConform Time InitMethodProbs \ Backrub 2 \ BigBackrub 1 \ FixOmega 1 \ OneRotamer 5 \ ClashingRotamer 1 \ ClusteredRotamer 1 \ CrossOver 1 \ CrossAndInsert 1\ CloseGap 1 \ MoveGap 1 \ HealGap 2 \ InsertFragment 1 \ InsertSpecificFragment 2 \ ReduceBreak 2 \ ReduceConstraint 2 \ ReduceClash 1 \ JiggleSegment 1 \ JiggleSubtree 1 \ OptAllSegments 1 \ OptSegment 1 \ OptSubtree 1 \ ShiftSegment 1 \ ShiftSubtree 1 \ TweakHbondSegment 1 \ TweakHbondSubtree 1 \ TweakPhiSegment 1 \ TweakPhiSubtree 1 \ TweakPsiSegment 1 \ TweakPsiSubtree 1 \ TweakPsiPhiSegment 1 \ TweakPsiPhiSubtree 1 OptConform pool_size 20 num_gen 60 gen_size 100 \ super_iter 1 super_num_gen 100 \ scwrl_each use_all keep_all NameConform T0397.try10-opt2 PrintConformPDB T0397.try10-opt2.pdb CostConform ScaleCost break 2 soft_clashes 5 CostConform Time OptConform pool_size 40 num_gen 60 gen_size 100 \ super_iter 2 super_num_gen 300 use_all NameConform T0397.try10-opt3 PrintConformPDB T0397.try10-opt3.pdb # PrintConformHbonds try10-opt3.all-hbonds # PrintConformHbonds nonhelix backbone try10-opt3.beta-hbonds PrintConformSheets try10-opt3.sheets PrintConformHelices try10-opt3.helices PrintConstraints all try10-opt3.constraints # PrintConformBreaks try10-opt3.breaks CostConform Time quit