-
-acolor <color>
-
-add_interactions
-
-add_receptors
-
-add_style
-
-addbox <distance> [No Default]
-
-added_date <value>
-
-addfraglib
-
-addtorlib
-
-all <format>
-
-allow_truncate
-
-allowed_clashes
-
-allowedClashes
-
-altloc <method>
-
-am1bcc
-
-annotate_scores [Default: false]
-
-apo_box <filename>
-
-apo_coords
-
-apo_grids
-
-apo_point_grid
-
-append
-
-append <bool>
-
-aromstyle <style>
-
-around <filename>
-
-around_mol <filename>
-
-aScale)
-
-assignCCP4
-
-astl <style>
-
-at_coords <filename>
-
-atomcolor <color>
-
-atomsstl <style>
-
-atomstereostyle <style>
-
-attachColor
-
-attachFrag
-
-attachmentCutoff (-attachcut)
-
-attachmentScale (-attach
-
-autoMTZ
-
-autoMTZ <true or false>
-
-autoThenManualSearch
-
-base <NAME>
-
-bb_clash_threshold <value>
-
-bbox <xmin> <ymin> <zmin> <xmax> <ymax> <zmax>
-
-bcolor <color>
-
-best_Receptor_Pose_Only
-
-besthits <N>
-
-besthits N
-
-biggerisbetter
-
-blobsThenBox
-
-blobTanimoto
-
-bondcolor <color>
-
-bondOrder (-bo)
-
-bondsstl <style>
-
-bondstereostyle <style>
-
-boundary <number>
-
-boundary_radius <number>
-
-boundary_spacing <number>
-
-bounding_box <xmin> <ymin> <zmin> <xmax> <ymax> <zmax>
-
-Box
-
-box <box file> [No Default]
-
-box <filename>
-
-box_mol <filename>
-
-boxpad <number>
-
-bu_superpose
-
-build_cterm_caps
-
-build_disulfidebridges <value>
-
-build_loops
-
-build_nterm_caps
-
-build_sidechains
-
-build_with_crystalpacking
-
-buildff
-
-bumpRadius
-
-by <number>
-
-calc <run_type>
-
-canonOrder
-
-cap_delete_clashing_solvent
-
-capAttach
-
-ch3
-
-chain <letter>
-
-chainid <chainid>
-
-charge_radii
-
-charges
-
-Check
-
-checkBond (-checkbond)
-
-checkGeometry
-
-chemff <cff_file>
-
-chemff <cffname>
-
-chunksize M
-
-ciftype
-
-clamp_at_level
-
-clashed_molecule_file <filename>
-
-clean <bool>
-
-clear_score_cache [Default: false]
-
-cofactor_codes <codes>
-
-collapse_nonsite_alts
-
-cols <number>
-
-commentEnergy
-
-complex <filename>
-
-conflabel
-
-coords <filename>
-
-count
-
-countConfs
-
-cpddb
-
-cplx_grids
-
-crop_length <value>
-
-csv
-
-current_charges
-
-cutoff <F>
-
-cutoff <float>
-
-cutoff <number>
-
-cutoff <score>
-
-database <filename>
-
-db (-database)
-
-dbase <filename>
-
-dbase <input filename1> [<input filename2> ... ]
-
-dbase <input filename1> [<input filename2> ...]
-
-dcutoff <number>
-
-default <number>
-
-default_value <number>
-
-deleteFixHydrogens
-
-densityAsIs
-
-dielectric_model <type>
-
-dir <path>
-
-disable_all_custom_constraints [Default: false]
-
-disable_all_protein_constraints [Default: false]
-
-disable_custom_constraint <constraint> [<constraint> ...] [No Default]
-
-disable_protein_constraint <name> [<name> ...] [No Default]
-
-distance <value>
-
-distance_cutoff <number>
-
-dock_resolution <setting> [Default: Standard]
-
-docked_molecule_file <filename>
-
-docked_molecule_file <filename> [Default: docked.oeb.gz]
-
-docked_molecule_file <filename> [Default: docked.oeb.gz]
-
-docked_poses <filename>
-
-dots
-
-du <filename>
-
-duplicate_removal
-
-eganEgg (-egan)
-
-enable_all_custom_constraints [Default: false]
-
-enable_all_protein_constraints [Default: false]
-
-enable_custom_constraint <constraint> [<constraint> ...] [No Default]
-
-enable_protein_constraint <name> [<name> ...] [No Default]
-
-ensemble
-
-entropy <type>
-
-enum_cofactors_sites
-
-enumBridgehead
-
-enumEZ
-
-enumNitrogen
-
-enumRing
-
-enumRS
-
-enumSpecifiedStereo
-
-eon_input
-
-eon_input_file <filename>
-
-eon_input_size <N>
-
-eon_maxconfs <N>
-
-eps_in <number>
-
-eps_out <number>
-
-erange
-
-ET (-et)
-
-ewindow
-
-exact_vdw
-
-excipient_codes
-
-exclude_reg_ss <value>
-
-excludeDUligand
-
-excludeDUsolvent
-
-extract_custom_constraints <filename> [No Default]
-
-fail
-
-Fc <columnname>
-
-Fdelwt <columnname>
-
-ff
-
-ff [Default: ff14sb_parsley]
-
-ff <type>
-
-fileChrg
-
-filter
-
-fit <filename>
-
-fit_lig <filename>
-
-fix_file <filename>
-
-fix_serial_numbers
-
-fix_smarts <file_name>
-
-fixfile
-
-fixpka_dbase
-
-fixpka_query
-
-fixrms
-
-fixsmarts
-
-fixup_pepflips <true or false>
-
-fixup_rotamers <true or false>
-
-fixup_shapefit_residues <true or false>
-
-flatten
-
-flex_file <filename>
-
-flexdist <d>
-
-flexlist <fn>
-
-flexRange [Default: 2.0]
-
-flextype <type>
-
-flip_bias_scale
-
-flipN
-
-flipper
-
-flipper_maxcenters
-
-flipper_warts
-
-Fobs <columnname>
-
-forceExistingResidueNames
-
-forcefield
-
-forceFlip
-
-format
-
-fragment
-
-fromCT
-
-Fwt <columnname>
-
-g <name>
-
-generate_tautomers
-
-geq <number>
-
-geq_mask <number>
-
-grad_conv <c>
-
-gradTol [Default: 1.0e-6]
-
-grid
-
-grid <name>
-
-grid1 <name>
-
-grid2 <name>
-
-grid3 <name>
-
-grid_spacing <number>
-
-grids <type>
-
-harm_constr1 <k>
-
-harm_constr2 <d>
-
-harm_smarts <file.txt>
-
-heavy_rms
-
-het_group_nbr_dist <value>
-
-hitinterval
-
-hitlist_size <num> [Default: 500]
-
-hitlist_size <num> [Default: 500]
-
-hitlistProt
-
-hitsfile <filename>
-
-i <filename>
-
-i <filename>
-
-idea (-cluster)
-
-ignore_nitrogen_stereo
-
-in
-
-in (-i)
-
-in <directory>
-
-in <filename>
-
-in <molecule file>
-
-in <proteinfile>
-
-in1 (-i1)
-
-in1 <filename>
-
-in2 (-i2)
-
-in2 <filename>
-
-in3 <filename>
-
-incl_SA_term <value>
-
-incl_solvation <value>
-
-includeInput
-
-includePackingResidues
-
-includeRotors
-
-info
-
-inner_dielectric <d>
-
-inner_dielectric <number>
-
-input <filename>
-
-input_file1 <filename>
-
-input_file2 <filename>
-
-input_file3 <filename>
-
-input_mol <filename>
-
-inscode <letter>
-
-int_method <value>
-
-interval
-
-ionic <type>
-
-ionize
-
-iteration_cycle_size
-
-keep_hydrogens
-
-keepFailures
-
-l <filename>
-
-largest_part
-
-legend <bool>
-
-leq <number>
-
-leq_mask <number>
-
-lig_box <filename>
-
-lig_coords
-
-lig_grids
-
-lig_point_grid
-
-ligand <filename>
-
-ligand_names <names>
-
-ligandAsIs
-
-ligandCharge [Default: current]
-
-ligands <filename>
-
-light_background
-
-light_bkg
-
-like_apo <filename>
-
-like_box <filename>
-
-like_lig <filename>
-
-like_std <filename>
-
-linkOnly (-linkonly
-
-lipid_codes <codes>
-
-loadPG <filename>
-
-log
-
-log <filename>
-
-log <logfile>
-
-log <prefix>
-
-logfile <filename>
-
-lookup
-
-loop_clash_threshold <value>
-
-loop_db_filename <filename>
-
-loop_distance_buffer <value>
-
-make_packing_residues
-
-manualSearch <filename>
-
-map <filename>
-
-map <mtz file>
-
-mask_cutoff <number>
-
-mask_vdw
-
-masked_point_cutoff <number>
-
-max
-
-max_bu_atoms
-
-max_bu_parts
-
-max_eval_loops <value>
-
-max_hits <value>
-
-max_iter <m>
-
-max_iterations
-
-max_length <value>
-
-max_lig_atoms
-
-max_lig_residues
-
-max_sys_atoms
-
-maxABS)
-
-maxAcceptors)
-
-maxAromFJCt
-
-maxCenters
-
-maxChiral
-
-maxComplexity (-maxComp)
-
-maxConfRange
-
-maxconfs
-
-maxconfs <N>
-
-maxconfs <value>
-
-maxDegree
-
-maxDonors)
-
-maxFrag
-
-maxFrequency (-maxFreq)
-
-maxFsp3C
-
-maxgenerated
-
-maxHit (-maxhit)
-
-maxhits <N>
-
-maxHvy
-
-maxHvyAtom (-maxHeavyAtom)
-
-maxIter [Default: 1000]
-
-maxLipinski
-
-maxLipinskiAcc (-maxLipinskiAcceptors
-
-maxLipinskiDon (-maxLipinskiDonors
-
-maxLocalStrain
-
-maxlogp
-
-maxMartin (-maxAbbott
-
-maxmatch
-
-maxMolWt
-
-maxMolWt (-maxmolecularweight)
-
-maxpages
-
-maxpsa (-maxtpsa)
-
-maxrot
-
-maxRotBond (-maxRotatableBond)
-
-maxtautomericatoms
-
-maxtime
-
-maxtoreturn
-
-maxzonesize
-
-mcquery
-
-merge <number>
-
-metadata <filename>
-
-method <method>
-
-method <value>
-
-method {option}
-
-min_align_score
-
-min_lig_atoms
-
-minABS)
-
-minAcceptors)
-
-minAromFJCt
-
-minComplexity (-minComp)
-
-minDegree
-
-minDonors)
-
-minFrequency
-
-minFrequency (-minFreq)
-
-minFsp3C
-
-minHvy
-
-minHvyAtom (-minHeavyAtom)
-
-minimum_probability
-
-minimum_rscc <number>
-
-minimum_rscc_increase <number>
-
-minLipinski
-
-minLipinskiAcc (-minLipinskiAcceptors
-
-minLipinskiDon (-minLipinskiDonors
-
-minlogp
-
-minMartin (-minAbbott
-
-minMolWt (-minmolecularweight)
-
-minpsa (-mintpsa)
-
-minRotBond (-minRotatableBond)
-
-MMFF94s
-
-mmff94s
-
-mod_vdw
|
-
-model <type>
-
-mol <filename>
-
-molNames
-
-molnames
-
-molnames <input filename> [No Default]
-
-mpi_hostfile
-
-mpi_hostfile <filename>
-
-mpi_np
-
-mpi_np <n>
-
-mpi_np <number>
-
-mtype
-
-mtype <setting>
-
-mtz <mtz file>
-
-names <molecule name> [<molecule name> ...] [No Default]
-
-nchunks N
-
-ncpu
-
-ncpu <value>
-
-negImageType [Default: standard]
-
-neglect_frozen
-
-neutralpH
-
-new_value <number>
-
-newrule
-
-no_dots
-
-no_dots [Default: false]
-
-no_extra_output_files
-
-no_extra_output_files [Default: false]
-
-no_extra_output_files [Default: false]
-
-no_prep
-
-no_table
-
-noCoulomb
-
-noqueryprot (-noqueryprotein)
-
-noqueryselection)
-
-noqueryselectprot (-noqueryselectionprotein
-
-normalize
-
-normalize_and_rescore <bool>
-
-nostructs
-
-nostructs [Default: false]
-
-num_orientations <number>
-
-num_poses
-
-num_poses <num> [Default: 1]
-
-o <filename>
-
-o <filename>
-
-oformat <extension>
-
-omega
-
-op <value>
-
-operation <value>
-
-opt
-
-opt_expt_protons
-
-opt_shell <value>
-
-opt_stage1_iter_multiplier <value>
-
-opt_stage2_iter_multiplier <value>
-
-opt_tolerance <value>
-
-optchem
-
-optDOF
-
-optdof
-
-optGeometry <dof>
-
-optimize [Default: cartesian]
-
-optimize <level> [No Default]
-
-optMethod <type>
-
-out
-
-out (-o)
-
-out <filename prefix>
-
-out <filename>
-
-out <oebfile>
-
-out <out>
-
-out <prefix>
-
-out <protein>
-
-out_complex <filename>
-
-out_protein <filename>
-
-outer_dielectric <number>
-
-outprot
-
-output <filename>
-
-output_all_format <format>
-
-output_grid <filename>
-
-output_mol <filename>
-
-outputall
-
-outputdir
-
-outputdir <dirname>
-
-outputquery
-
-overlays
-
-overwrite
-
-overwrite (-over)
-
-p <filename>
-
-pad_zeros
-
-padding
-
-pagesize <size>
-
-param
-
-param <filename>
-
-param <param_file>
-
-param <parameter filename>
-
-param <parameter filename> [No Default]
-
-param <paramfile>
-
-paramfile
-
-PBsolvent_dielectric <value>
-
-pendingFile
-
-Phic <columnname>
-
-Phidelwt <columnname>
-
-Phiwt <columnname>
-
-pkanorm
-
-planarAniline
-
-point_grid
-
-precheck
-
-pref_author_record
-
-prefix
-
-prefix <file prefix>
-
-prefix <filename prefix>
-
-prefix <name>
-
-prefix <p>
-
-prefix <pn>
-
-prefix <prefix>
-
-prefix <text>
-
-prefix <value> [Default: hybrid]
-
-prefix <value> [Default: fred]
-
-prefix <value> [Default: rescore]
-
-prepare_score_cache <fred
-
-primaryFrag
-
-progress
-
-progress : Shows a progress bar
-
-progress <method>
-
-progress <style>
-
-properties <type>
-
-property (-prop)
-
-prot (-protein)
-
-prot <filename>
-
-protein
-
-protein <filename>
-
-protein_elec <m>
-
-protein_vdw <r>
-
-proteinMask
-
-protonate
-
-psize <size>
-
-qconflabel
-
-query <filename>
-
-queryFragment (-queryFrag)
-
-queryMol (-qMol)
-
-quickLook (-quick)
-
-radii <type>
-
-randomstarts <N>
-
-rangeIncrement
-
-rangeOffset
-
-rangeSize
-
-rank
-
-rankby <score>
-
-rankby <SD tag>
-
-readConfs
-
-receptor <filename> [<filename> ...]
-
-receptor <filenames>
-
-receptor <receptor file1> [<receptor file2> ...]
-
-receptor <receptor file>
-
-receptors <filenames>
-
-ref <filename>
-
-ref_lig <filename>
-
-ref_tolerance
-
-refmol <filename>
-
-rejected_file
-
-relax
-
-removeDuplicates (-duplicates)
-
-report
-
-report <filename>
-
-report_file
-
-report_file <filename> [Default: docking_report.pdf]
-
-report_file <filename> [Default: report.txt]
-
-reportFile <filename>
-
-reportfile <filename>
-
-reporthtml
-
-res <number>
-
-rescored_mol_output_file <output filename> [Default: scored.oeb.gz]
-
-residue_chain <letter>
-
-residue_insert <letter>
-
-residue_number <number>
-
-residueID [Default: None]
-
-residues
-
-resname <name>
-
-resolution <level>
-
-restrict_calc <level>
-
-restrict_to_refsite
-
-results_set <type>
-
-ringOnly (-ring)
-
-rms
-
-rms <value>
-
-rmsrange
-
-rot <number>
-
-rot_coverage <value>
-
-rot_library <value>
-
-rotorOffsetCompress
-
-rows <number>
-
-rsr
-
-salt
-
-salt <c>
-
-salt <number>
-
-salt_conc <number>
-
-sampleHydrogens
-
-save_component_scores [Default: false]
-
-savePG <filename>
-
-sc_delete_clashing_solvent
-
-scale
-
-scale <number>
-
-scatter
-
-scdbase
-
-score_file
-
-score_file <filename> [Default: score.txt]
-
-score_tag
-
-score_tag <score tag> [No Default]
-
-score_tag <tag> [No Default]
-
-score_tag <tag> [No Default]
-
-scoreonly
-
-sd_tags <Tag> [<Tag> ...] [No Default]
-
-sdEnergy
-
-sdtag
-
-sdtag <string>
-
-sdTags
-
-searchff
-
-select
-
-select (-selection)
-
-separate
-
-sequence_cutoff <float>
-
-set_custom_constraints <filename> [No Default]
-
-setfraglib
-
-settings <settingsfile>
-
-settings_file
-
-settings_file <filename> [Default: settings.param]
-
-settorlib
-
-shapeCutoff
-
-shapeonly
-
-shefA <a>
-
-shefB <b>
-
-sheffield
-
-silent
-
-site_residue <filename>
-
-site_residue <residue identifier>
-
-site_size <value>
-
-site_size: <value>
-
-size <size>
-
-slice
-
-smarts
-
-smiles_file <filename> [No Default]
-
-solv_dielectric <d>
-
-solvcharges <type>
-
-solvent <type>
-
-solventCA <s>
-
-solventPB
-
-sort_poses [Default: false]
-
-sortAllChiral <true/false>
-
-sortBy
-
-source_date <value>
-
-source_name <value>
-
-sp3_aromatic <bool>
-
-sp3aromatic <bool>
-
-space <number>
-
-spacing
-
-split
-
-split_lig
-
-stabilization
-
-stabilization <bool>
-
-standard_grids
-
-startfact
-
-stats
-
-status
-
-status_file
-
-status_file <filename> [Default: status.txt]
-
-statusfile
-
-statusfile <filename>
-
-stbl
-
-stbl <bool>
-
-std_box <filename>
-
-std_coords
-
-std_grids
-
-stereo
-
-strict
-
-strict_proline_match
-
-strictatomtyping
-
-strictfrags
-
-strictstereo
-
-strip_water
-
-struc
-
-struct)
-
-subrocs
-
-subtan
-
-superpose
-
-superpose_method : <method>
-
-superpose_method <method>
-
-suppressH
-
-surf
-
-surface <bool>
-
-surface_points
-
-szmap_mpi_hostfile <filename>
-
-szmap_mpi_np <number>
-
-t
-
-t <prop>
-
-table
-
-table <filename>
-
-tableFlag
-
-tag_set <set>
-
-tagname <prop>
-
-tanimoto_cutoff <F>
-
-target
-
-target <filename>
-
-targetMask
-
-targetMask [Default: targetComplexNoSolvent]
-
-targetPred
-
-tautomer
-
-title
-
-title <text>
-
-title <title>
-
-to <number>
-
-tor_constr <fn>
-
-torlibtype
-
-track <filename>
-
-transform_threshold <value>
-
-turn_inner_contour <on or off> [No Default]
-
-type
-
-typecheck
-
-umatch
-
-undocked_molecule_file
-
-undocked_molecule_file <filename> [Default: undocked.oeb.gz]
-
-unique
-
-use_apo_from <filename>
-
-use_gpu <bool>
-
-useGPU
-
-userFrags
-
-userUnique
-
-v
-
-value_cutoff <number>
-
-vcutoff <number>
-
-vdw_cutoff
-
-vdw_scale <number>
-
-veber (-gsk)
-
-verbose
-
-verbose (-v)
-
-verbose :
-
-verbose : Triggers copious logging output
-
-verbose <true or false>
-
-warn_if_missing_hydrogens
-
-warts
-
-water_charge <type>
-
-write_biounits
-
-writeFullDict
-
-writegrid
-
-zap_spacing <number>
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