############################################################################ # # ####################### OCKER Parameter File ############################ # # ############################################################################ ############################################################################ # ######################### Workflow Parameters ########################### jobtype = "shapeFlexibleDocking" ##Workflow to be used, ##valid options: ##jobtype = "shapeFlexibleDocking" ##jobtype = "shapeFlexibleDockingWithQuery" ##jobtype = "shapeFlexibleDockingWithFlexibleProtein" ##jobtype = "shapeFlexibleOverlayAndOptimize" ##jobtype = "scoreProteinLigandComplex" ##jobtype = "scoreMultipleProteinLigandComplex" ##jobtype = "setupLigandDatabase" ##jobtype = "setupOcker" ##jobtype = "convertReceptor" ##jobtype = "ockerResultsRanking" ############################################################################ # ######################### Input Parameters ############################## proteinpdbFilename = "../ockerSetup/ockerReceptor.pdb" #Input protein pdb file. #ligandmol2Filename = "ligand.mol2" ##Input ligand mol2 file. referenceFilename = "../ockerSetup/molec000075.sdf" ##reference ligand file. Default none #queryFilename = "" ##Query file for inital alignment. Default none waterFilename = "../ockerSetup/water.pdb" ##Particle water filename. Default none sphereFilename = "../ockerSetup/ocker.sph" #Atpts sphere file containing site points ############################################################################ # ########################## OutPut Parameters ############################# ############################################################################ # ##################### General Docking Parameters ########################## debug = True ##Turn debugging on. Default: False #------------------------Placement Parameters------------------------------- minBumpScore = "10.0" #Minimum bump score a pose must score below, Default 1.0 #larger sites need a bigger bump score #combinationMethod = "sum" ##Scoring functions combination method to be used during poise selection ##Default: sum ##Options: sum product nonlinear tabuListSize = "100" ##Length of tabu list. Default: 20 numberOfPoises = "25" ##Number of final poises returned. Default: 20 #xtal = "True" ##Use xtal, aka input ligand conformation. Default: False #exhaustiveConformerGeneration = True ##ExhaustiveConformerGeneration for conformer overlay. Default: False #validation = "True" ##Print out information used in validation testset. Default: False #bestMatchPerConformer = "True" ##Keep only the best color match per conformer. Default: True #preBuiltConformers = "True" ##Use preBuilt conformers for docking, i.e do not generate internal conformers #----------------------- Constraint Options -------------------------------- #constraintFilter = "True" ##Use constraint filter during docking. Default False #constraintScore = "True" ##Use constraint score during scoring. Default False #requiredAtomIdConstraintList = "111,692,708,716,692,708,1094,692,698,704" ##Comma separated list of atom numbers for constraint. optionalAtomIdConstraintList = "111,692,708,716,692,708,1094,692,698,704" ##comma separated list of atom numbers for optional constraint. #------------------------- Scoring Options --------------------------------- #scoringFunctions = 'all' ##Scoring functions to be used during poise selection, comma separated. ##Default: all bump = "True" ##Use bump scoring function during poise selection. Default: False autodock = "True" ##Use autodock scoring function during poise selection. Default: False #chemscore = "True" ##Use chemscore scoring function during poise selection. Default: False score = "True" ##use score (PK) scoring function during poise selection. Default: False quality = "True" ##Use quality scoring function during poise selection Default: False #smog = "True" ##Use smog scoring function during poise selection. Default: False #smog_h = "True" ##use smog_h scoring function during poise selection. Default: False pmf = "True" #Use pmf scoring function during poise selection. Default: False pmf_rb = "True" ##Use pmf_rb scoring function during poise selection. Default: False #docknrg = "True" ##Use dock scoring function during poise selection. Default: False #surflex = "True" ##Use surflex scoring function during poise selection. Default: False #mmff = "True" ##Use mmff scoring function during poise selection. Default: False #comboscore = "True" ##Use comboscore scoring function during poise selection. Default: False #fitversky = "True" ##Use fitversky scoring function during poise selection. Default: False #tversky = "True" ##Use tversky scoring function during poise selection. Default: False #tanimoto = "True" ##Use tanimoto scoring function during poise selection. Default: False scaledcolor = "True" ##Use scaledcolor scoring function during poise selection. Default: False #colorscore = "True" ##Use colorscore scoring function during poise selection. Default: False overlap = "True" ##Use overlap scoring function during poise selection. Default: False #------------------------Post Docking Options------------------------------- refineFinalPoises = "True" ##Refine final poises with mmff94 for selection. Default: False #usePBSolventRefinement = "True" ##Use OEProteinElectrostatics_SolventPB_forces during final minimisation. Default: False #flexibleProteinDuringRefinement = "True" ##Treat residues of protein flexibly during refinement. Default: False #flexibleProteinRefinementDistance = "1.0" ##Protein residues within distance of ligand are flexible. Default: 2.0 writeFinalPoise = "True" ##write final best MMFF poise after docking. Default: False #-----------------------Output Options-------------------------------------- writeDockedPoises = "True" ##write final docked (not refined) poises writeRefinedPoises = "True" ##Write final docked + refined poises. finalCombinationMethod = "sum" ##Combination method to be used during final poise selection ##Options: sum, product, nonlinear ############################################################################ # ################## Workflow Specific Parameters ######################## #-------------------------shapeBasedDocking--------------------------------- #shapeMatchOnly = "True" ##Use shape matching to points, a'la dock sans color. Default: False #numMatchesPerConformer ##NumMatchesPerConformer using during shape overlay #colorForceFieldType ##ColorForceFieldType, 0: OEColorFFType_ExplicitMillsDean, 1: OEColorFFType_ImplicitMillsDean #readCffFromFile = "generation_5_352.cff" ##readCffFromFile rather than using built in CFF #--------------------FlexibleProteinDocking--------------------------------- #----------------General Parameters------------------------------------- #flexibleProtein = "True" #Use flexible protein segments during docking. Default: False #----------------Pregenerated External Conformation Parameters---------- #i.e complete protein structures with loops spliced in, #typically from alternative xtal structures, or NMR, or MD.... #useExternalReceptorEnsembleConformations = "True" ##Read receptor external conformations from prexisting files. Default: False #externalReceptorEnsembleList = "1m48_chainA_fitted.pdb,1qvn_chainA_fitted.pdb" ##List of [proteinPdbFileName, ] for receptor conformations. #--------------Pregenerated External Loop Parameters-------------------- #readExternalLoopConformations = "True" ##Read flexible loops generated by external method. Default: False #loopSimilarityThreshold = "0.3" ##Minimum rmsd a pair of resiudes must be greater than to be considered different Default 0.3 #flexibleProteinMinBumpScore = "1.00" ##Minimum self bump score a loop must have to be kept. Default: 1.00 flexibleProteinScoringFunctions = "pmf" ##Scoring functions to be used during protein loop selection. #flexibleProteinReceptorResIdList = " 1z92_chainA_reference.pdb: A | ASN 33 - TYR 45 + GLU 61 - ALA 73 " ##List of [proteinPdbFileName, residue numbers] for flexibilty nested list. ##The segments on the protein receptor that will be replaced with the loops taken from ##the loop files specified in externalProteinLoopList #flexibleProteinResIdList = "1m48_chainA_fitted.pdb: A | ASN 33 - TYR 45 + GLU 61 - ALA 73 " ##list of [proteinPdbFileName, residue numbers] for flexibilty where loops are taken from, nested list #-------------Generate Loop Parameters-------------------------------------- #loopGenerationMethod = "direx" ##loop generation method. valid options are omega and direx. Default: omega #loopSimilarityThreshold = "0.3" ##Minimum rmsd a pair of resiudes must be greater than to be considered different Default 0.3 #flexibleProteinMinBumpScore = "1.00" ##Minimum self bump score a loop must have to be kept. Default: 1.00 #flexibleProteinScoringFunctions = "pmf" ##Scoring functions to be used during protein loop selection. #flexibleProteinReceptorResIdList = " 1z92_chainA_reference.pdb: A | ASN 33 - TYR 45 + GLU 61 - ALA 73 " ##List of [proteinPdbFileName, residue numbers] for flexibilty nested list. ##The segments on the protein receptor that will be replaced with the loops taken from ##the loop files specified in externalProteinLoopList #flexibleProteinResIdList ##list of [proteinPdbFileName, residue numbers] for flexibilty where loops are taken from, nested list. #flexibleProteinResIdList = " 1z92_chainA_reference.pdb: A | ASN 33 - TYR 45 + GLU 61 - ALA 73 " ##flexibleProteinResIdList = " 1m48_chainA_fitted.pdb: A | ASN 33 - TYR 45 + GLU 61 - ALA 73 , 1py2_chainA_fitted.pdb: A | ASN 30 - TYR 45 + GLU 61 - ALA 73 " #flexibleProteinResIdList = " 1ir1_aligned.pdb: A | ASN 33 - TYR 45 + GLU 61 - ALA 73" #flexibleProteinResIdList = " 1m47_fitted.pdb: A | ASN 33 - TYR 45 + GLU 61 - ALA 73 " #flexibleProteinResIdList = " 1m48_chainA_fitted.pdb: A | ASN 33 - TYR 45 + GLU 61 - ALA 73 " #flexibleProteinResIdList = " 1m49_chainA_fitted.pdb: A | ASN 33 - TYR 45 + GLU 61 - ALA 73 " #flexibleProteinResIdList = " 1m4a_fitted.pdb: A | ASN 33 - TYR 45 + GLU 61 - ALA 73 " #flexibleProteinResIdList = " 1m4b_fitted.pdb: A | ASN 33 - TYR 45 + GLU 61 - ALA 73 " #flexibleProteinResIdList = " 1m4c_chainA_fitted.pdb: A | ASN 33 - TYR 45 + GLU 61 - ALA 73 " #flexibleProteinResIdList = " 1nbp_fitted.pdb: A | ASN 33 - TYR 45 + GLU 61 - ALA 73 " #flexibleProteinResIdList = " 1pw6_chainA_fitted.pdb: A | ASN 33 - TYR 45 + GLU 61 - ALA 73 " #flexibleProteinResIdList = " 1py2_chainA_fitted.pdb: A | ASN 30 - TYR 45 + GLU 61 - ALA 73 " #flexibleProteinResIdList = " 1qvn_chainA_fitted.pdb: A | ASN 33 - TYR 45 + GLU 61 - ALA 73 " #flexibleProteinResIdList = " 1z92_chainA_reference.pdb: A | ASN 33 - TYR 45 + GLU 61 - ALA 73 " #flexibleProteinResIdList = " 3ink_chainC_fitted.pdb: C | ASN 33 - TYR 45 + GLU 61 - ALA 73 " #Everything #flexibleProteinResIdList = "1ir1_aligned.pdb: A | ASN 33 - TYR 45 + GLU 61 - ALA 73, 1m47_fitted.pdb: A | ASN 33 - TYR 45 + GLU 61 - ALA 73, 1m48_chainA_fitted.pdb: A | ASN 33 - TYR 45 + GLU 61 - ALA 73,1m49_chainA_fitted.pdb: A | ASN 33 - TYR 45 + GLU 61 - ALA 73, 1m4a_fitted.pdb: A | ASN 33 - TYR 45 + GLU 61 - ALA 73, 1m4b_fitted.pdb: A | ASN 33 - TYR 45 + GLU 61 - ALA 73, 1m4c_chainA_fitted.pdb: A | ASN 33 - TYR 45 + GLU 61 - ALA 73, 1nbp_fitted.pdb: A | ASN 33 - TYR 45 + GLU 61 - ALA 73, 1pw6_chainA_fitted.pdb: A | ASN 33 - TYR 45 + GLU 61 - ALA 73 , 1py2_chainA_fitted.pdb: A | ASN 30 - TYR 45 + GLU 61 - ALA 73, 1qvn_chainA_fitted.pdb: A | ASN 33 - TYR 45 + GLU 61 - ALA 73, 1z92_chainA_reference.pdb: A | ASN 33 - TYR 45 + GLU 61 - ALA 73,3ink_chainC_fitted.pdb: C | ASN 33 - TYR 45 + GLU 61 - ALA 73 " #-----------------------Database Conversion--------------------------------- #inputLigandDatabaseFilename ##Input ligands for database conversion. #-----------------------Convert Receptor------------------------------------ #proteinpdbFilename ##Input pdb filename to be converted to a empty ocker receptor . #convertedpdbFilename ##Output filename for converted receptor file. Default OckerReceptor.pdb #---------------------- Setup Ocker ------------------------------------- #atptsNearList ##Near list for atpts points, format: A | ASN 33 , TYR 45 , GLU 61 , ALA 73) #bumpCheck = "True" ##Check for points within bump distance of receptor. Default True #polarContact = "2.2" ##polarContact distance for point generation. Default 2.2 #carbonContact = "2.8" ##carbonContact distance for point generation. Default 2.8 #closeDistance = "1.0" ##closeContact distance for point generation. Default 1.0 #ligandPointDistance = "2.0" ##ligandPoint distance for point to be kept. Default 2.0 #---------------------- OckerResultsRanking ---------------------------- ##ockerResultsRanking options #knownActivesIDList = "" ##List of LigandID's of known actives in flat file #knownDatabase = "" ##Database (mol2, sdf) of molecules whose names are LigandID's of known actives #knownOckerOut = "" ##Ocker.out file of results for known actives #resultsOckerOut = "" ##Ocker.out file containing results to be rank ordered #databaseIndexFileName = "" ##Ocker databaseIndexFileName containing Name functional group string, rotatablebond count, molecular weight ############################################################################