{
  "licenseDirectoryPath" : "$LICENSES",$LOGFILE
  "Initialization" : {
     "allowMissingTerminals": true,
     "ForceField" : "$FORCEFIELD",
     "MultipleComplex": [ $COMPLEXES ],
     "Solvent" : {
        "ionicStrength" : 0.15, "solventType" : "$SOLVENT", "useDebyeLength" : true }
   },
   "verboseMode": true,
   "commands" : [
      {
         "commandType" : "peleSimulation",
         "RandomGenerator" : { "seed" : $SEED },$SELECTION_TO_PERTURB
         "PELE_Output" : {
            "savingFrequencyForAcceptedSteps" : 1,
            "savingMode" : "savingTrajectory",
            "reportPath": "$OUTPUT_PATH/$REPORT_NAME",
            "trajectoryPath": "$OUTPUT_PATH/$TRAJ_NAME"$INTER_STEP_LOGGER
         },
         "PELE_Parameters" : {$MINIMUM_STEPS
            "anmFrequency" : 0,
            "sideChainPredictionFrequency" : 2,
            "minimizationFrequency" : 1,
            "waterPerturbationFrequency": $WATER_FREQ,
            "perturbationCOMConstraintConstant" : $COM,$COMFPERT_FREQ
            "sideChainPredictionRegionRadius" : $SIDECHAIN_RADIUS,
            "activateProximityDetection": $PROXIMITY,
            "temperature": $TEMPERATURE,
            "numberOfPeleSteps": $PELE_STEPS
         },$CONSTRAINTS$PERTURBATION$SIDECHAIN_PERTURBATION$CONFORMATION_PERTURBATION
         "ANM" : {
            "algorithm": "CARTESIANS", "nodes": { "atoms": { "names": [ "_CA_" ]} },$PCA
            "ANMMinimizer" : {
               "algorithm" : "TruncatedNewton",
               "parameters" : {
                  "MaximumMinimizationIterations" : 1,
                  "MaximumNewtonIterations" : 25,
                  "MinimumRMS" : 0.2,
                  "alphaUpdated" : false,
                  "nonBondingListUpdatedEachMinStep" : false
               }
            },
            "options" : {
               "directionGeneration" : "$ANM_DIRECTION",
               "modesMixingOption" : "$ANM_MIX_MODES",
               "pickingCase" : "$ANM_PICKING_MODE"
            },
            "parameters" : {
               "displacementFactor" : $ANM_DISPLACEMENT,
               "eigenUpdateFrequency" : 1000000,
               "mainModeWeightForMixModes" : 0.75,
               "modesChangeFrequency" : $ANM_MODES_CHANGE,
               "numberOfModes": $ANM_NUM_OF_MODES,
               "relaxationSpringConstant" : $ANM_RELAXATION_CONST
            }
         },$WATER
         "SideChainPrediction" : {
            "algorithm" : "zhexin",
            "parameters" : { "discardHighEnergySolutions" : false, "resolution": $SIDECHAIN_RESOLUTION, "randomize" : false, "numberOfIterations": 1 },
            "selectionToOmit": {
               "links": {
                  "ids": [
                     "C:417",
                     "C:667",
                     "C:654",
                     "C:438",
                     "C:172",
                     "C:663",
                     "C:666",
                     "C:635",
                     "C:573",
                     "C:625",
                     "C:171",
                     "C:440",
                     "C:409",
                     "C:622",
                     "C:174",
                     "C:412",
                     "C:350",
                     "C:634",
                     "C:368",
                     "C:439",
                     "C:303",
                     "C:664",
                     "C:370",
                     "C:636",
                     "C:231",
                     "C:627",
                     "C:657",
                     "C:626",
                     "C:224",
                     "C:372",
                     "C:527",
                     "C:660",
                     "C:579",
                     "C:223",
                     "C:415",
                     "C:356",
                     "C:668",
                     "C:637",
                     "C:371",
                     "C:655",
                     "C:176",
                     "C:414",
                     "C:565",
                     "C:355",
                     "C:373",
                     "C:577",
                     "C:367",
                     "C:305",
                     "C:413",
                     "C:682",
                     "C:650",
                     "C:354",
                     "C:669",
                     "C:582",
                     "C:576",
                     "C:523",
                     "C:443",
                     "C:631",
                     "C:572",
                     "C:408",
                     "C:349",
                     "C:630",
                     "C:225",
                     "C:229",
                     "C:633",
                     "C:442",
                     "C:407",
                     "C:404",
                     "C:611",
                     "C:580",
                     "C:524",
                     "C:437",
                     "C:378",
                     "C:306",
                     "C:232",
                     "C:653",
                     "C:683",
                     "C:621",
                     "C:624",
                     "C:566",
                     "C:581",
                     "C:571",
                     "C:522"
                  ]
               }
            }
         },
         "Minimizer" : {
            "algorithm" : "TruncatedNewton",
            "parameters" : { "MinimumRMS" : 0.2, "alphaUpdated" : false, "nonBondingListUpdatedEachMinStep" : true }
         },
         "doNotIncludeInMinimization":
            {
             "links": {
                "ids": [
                   "C:417",
                   "C:667",
                   "C:654",
                   "C:438",
                   "C:172",
                   "C:663",
                   "C:666",
                   "C:635",
                   "C:573",
                   "C:625",
                   "C:171",
                   "C:440",
                   "C:409",
                   "C:622",
                   "C:174",
                   "C:412",
                   "C:350",
                   "C:634",
                   "C:368",
                   "C:439",
                   "C:303",
                   "C:664",
                   "C:370",
                   "C:636",
                   "C:231",
                   "C:627",
                   "C:657",
                   "C:626",
                   "C:224",
                   "C:372",
                   "C:527",
                   "C:660",
                   "C:579",
                   "C:223",
                   "C:415",
                   "C:356",
                   "C:668",
                   "C:637",
                   "C:371",
                   "C:655",
                   "C:176",
                   "C:414",
                   "C:565",
                   "C:355",
                   "C:373",
                   "C:577",
                   "C:367",
                   "C:305",
                   "C:413",
                   "C:682",
                   "C:650",
                   "C:354",
                   "C:669",
                   "C:582",
                   "C:576",
                   "C:523",
                   "C:443",
                   "C:631",
                   "C:572",
                   "C:408",
                   "C:349",
                   "C:630",
                   "C:225",
                   "C:229",
                   "C:633",
                   "C:442",
                   "C:407",
                   "C:404",
                   "C:611",
                   "C:580",
                   "C:524",
                   "C:437",
                   "C:378",
                   "C:306",
                   "C:232",
                   "C:653",
                   "C:683",
                   "C:621",
                   "C:624",
                   "C:566",
                   "C:581",
                   "C:571",
                   "C:522"
                ]
             }
         },
         "PeleTasks" : [
            {
               "metrics" : [$BE$SASA$NATIVE$METRICS$LOCAL_NONBONDING_ENERGY$COVALENT_SASA$MET_INTERACTION_RESTRICTIONS
                        { "tag" : "rand", "type" : "random" },
                        { "tag" : "rand4", "type" : "random" },
                        { "tag" : "rand3", "type" : "random" },
                        { "tag" : "rand2", "type" : "random" },
                        { "tag" : "rand1", "type" : "random" }
                     ]$PARAMETERS$INTERACTION_RESTRICTIONS
}]}]}