glide -k Command Help
Command: $SCHRODINGER/glide -k
AMIDE_MODE = option('penal', 'fixed', 'free', 'trans', 'generalized', default='generalized') # amide bond rotation behavior: "fixed", "free", "penal", "trans", "gen[eralized]"
AMIDE_TRANS_ALL = boolean(default=False) # include "nonstandard" amides in trans enforcement
AMIDE_TRANSTOL = float(default=20.0) # trans amide tolerance (in degrees)
ASL_RES_INTERACTION = string(default='') # If present, use it; else, use "radius_res_interaction."
ASLSTRINGS = string_list(default=list()) # ASL strings for receptor scaling
CALC_INPUT_RMS = boolean(default=False) # report RMS deviation against input geometry of each ligand
CANONICALIZE = boolean(default=True) # docking initiated from a canonical conformation per input ligand (false by default for HTVS precision)
COMPRESS_CSV = boolean(default=False) # compress file written when using WRITE_CSV
COMPRESS_POSES = boolean(default=True) # generate compressed maestro pose and _raw files
COMPRESS_REPORT = boolean(default=False) # Compress the HTML report for the docking job
CORE_ATOMS = int_list(default=list()) # index into reference ligand for each atom in core
CORE_DEFINITION = option('allheavy', 'allheavy_nostereo', 'smarts', 'mcssmarts', 'atomlist', default='allheavy') # how to define the ligand core: "allheavy" (default): generate a SMARTS from non-hydrogen atoms; "allheavy_nostereo": same, but ignoring stereochemistry; "smarts": user-specified SMARTS; "mcssmarts": generate SMARTS from maximum common substructure; "mcssmarts2": generate SMARTS with two disconnected cores from MCS; "atomlist": use the atoms listed in the s_rga_core_atoms structure property
CORE_FILTER = boolean(default=False) # skip ligands that do not contain the core
CORE_POS_MAX_RMSD = float(default=0.1) # maximum RMSD of core atom positions
CORE_RESTRAIN = boolean(default=False) # restrain core atoms
CORE_RESTRAIN_V = float(default=5.0) # strength of core restraining potential
CORE_SMARTS = string(default='') # SMARTS pattern to match for core RMSD calculation/restraint
CORE_SNAP = boolean(default=False) # When using core constraints ("CORE_RESTRAIN yes"): if "yes", use "snapping" core constraints algorithm. If "no", use filtering algorithm. If not set, choose automatically based on CORE_POS_MAX_RMSD ("yes" if < 0.75; "no" otherwise)
CORECONS_FALLBACK = boolean(default=False) # if a ligand fails to dock with CORE_SNAP retry it without
CSV_PROPS_FILE = string(default='') # file containing names of m2io properties to be added to csvfile
CV_CUTOFF = float(default=0.0) # Coulomb-van der Waals energy cutoff used for final filtering
DOCKING_METHOD = option('confgen', 'rigid', 'inplace', 'mininplace', default='confgen') # docking method: confgen=flexible docking; rigid=rigid docking; mininplace=refine (do not dock); inplace=score in place (do not dock)
DOINTRA = boolean(default=False) # relax bad intramolecular contacts
DOINTRA_SCALE = float(default=1.0) # scaling factor for intramolecular pose relaxation
DSCORE_CUTOFF = float(default=100.0) # Docking score cutoff
EPIK_PENALTIES = boolean(default=True) # include ligand Epik state penalties in the Glide DockingScore scoring function
EXPANDED_SAMPLING = boolean(default=False) # bypass elimination of poses in rough scoring stage (useful for fragment docking)
FLEXASL = string(default=None) # ASL defining flexible receptor atoms
FORCEFIELD = string(default='OPLS_2005') # force field
FORCEPLANAR = boolean(default=False) # trigger MMFFLD planarity options
GLIDE_CONFGEN_EFCUT = float(default=12.0, min=0.0) # energy cutoff during ligand conformer generation
GLIDE_CONS_FINALONLY = boolean(default=False) # only check for constraint satisfaction after docking is complete
GLIDE_DIELCO = float(default=2.0, min=0.0, max=9999.9) # dielectric constant
GLIDE_EXVOL_PENAL_NUM = float_list(default=list()) # maximum penalties in kcal/mol for each Glide excluded volume violation
GLIDE_EXVOL_PENAL_STRENGTH = option('low', 'small', 'medium', 'high', 'large', default='large') # penalty specification for (all) Glide excluded volumes.
GLIDE_NUMEXVOL = integer(default=0, min=0) # number of receptor excluded-volume regions
GLIDE_NUMUSEXVOL = integer(default=0, min=0) # number of excluded-volume regions to use
GLIDE_OUTPUT_USEHTOR = boolean(default=True) # use rotation of polar hydrogens as pose-distinguishing criterion
GLIDE_RECEP_ASLSCALE = boolean(default=False) # for Glide gridgen jobs, take per-atom charge and radius scaling factors from ASL specification
GLIDE_RECEP_MAESCALE = boolean(default=False) # for Glide gridgen jobs, take per-atom charge and radius scaling factors from properties written by Maestro to the receptor file
GLIDE_REFLIG_FORMAT = option('maestro', 'sd', 'mol2', default='maestro') # Glide reference ligand file format
GLIDE_REXVOL = float_list(default=list()) # sphere radii of Glide excluded volumes
GLIDE_REXVOLIN = float_list(default=list()) # inner sphere (max penalty) radii of Glide excluded volumes
GLIDE_XEXVOL = float_list(default=list()) # X-coordinates of centers of Glide excluded volumes
GLIDE_YEXVOL = float_list(default=list()) # Y-coordinates of centers of Glide excluded volumes
GLIDE_ZEXVOL = float_list(default=list()) # Z-coordinates of centers of Glide excluded volumes
GLIDECONSUSEMET = boolean(default=False) # use element-based metal radii for Glide constraints
GLIDERECEPTORSCALECHARGES = float_list(default=list()) # per-atom scale factors for receptor charges
GLIDERECEPTORSCALERADII = float_list(default=list()) # per-atom scale factors for receptor radii
GLIDESCORUSEMET = boolean(default=False) # use element-based metal radii in Glide scoring
GLIDEUSEALLEXVOL = boolean(default=False) # use all excluded volumes in file (as opposed to selected ones)
GLIDEUSEXVOL = boolean(default=False) # use excluded volumes
GLIDEUSEXVOLNAMES = string_list(default=list()) # excluded-volume labels to use in docking job
GLIDEXVOLNAMES = string_list(default=list()) # excluded-volume label list
GRID_CENTER = float_list(default=list(0.0, 0.0, 0.0)) # coordinates of the grid center
GRID_CENTER_ASL = string(default=None) # ASL expression defining the grid center
GRIDFILE = string(default='') # path to grid (.grd or .zip) file
GSCORE_CUTOFF = float(default=100.0) # GlideScore cutoff
HBOND_ACCEP_HALO = boolean(default=False) # include halogens as possible H-bond acceptors in scoring
HBOND_CONSTRAINTS = string_list(default=list()) # HBOND_CONSTRAINTS "hbond1 47", "hbond2 55"
HBOND_CUTOFF = float(default=0.0) # H-bond cutoff used for final filtering
HBOND_DONOR_AROMH = boolean(default=False) # include aromatic H as a possible H-bond donor in scoring
HBOND_DONOR_AROMH_CHARGE = float(default=0.0) # count aromatic H as a donor if its partial charge exceeds this value
HBOND_DONOR_HALO = boolean(default=False) # include halogens as possible H-bond donors in scoring
INCLUDE_INPUT_CONF = boolean(default=False) # include input conformation in confgen output
INCLUDE_INPUT_RINGS = boolean(default=False) # include input ring structures in confgen
INNERBOX = int_list(default=list(10, 10, 10)) # size of the box bounding the possible placements for the ligand centroid
KEEP_INPUT_CSV_FIELDS = boolean(default=False) # Keep the fields from the input ligand file when using WRITE_CSV
KEEP_SUBJOB_POSES = boolean(default=True) # keep <jobname>_subjob.poses.zip at the end of a distributed docking job
KEEPRAW = boolean(default=False) # do not delete the unsorted/unfiltered ("raw") pose file, <jobname>_raw.mae[gz]
KEEPSKIPPED = boolean(default=False) # save skipped ligands to <jobname>_skipped.mae[gz]
LIG_CCUT = float(default=0.15, min=0.0) # charge cutoff to determine whether to use vdW scaling of ligand atoms
LIG_MAECHARGES = boolean(default=False) # use charges from ligand Maestro file instead of those from the force field
LIG_VSCALE = float(default=0.8, min=0.0) # ligand vdW scaling (see also LIG_CCUT)
LIGAND_END = integer(default=0, min=0) # end ligand
LIGAND_INDEX = integer(default=None, min=1) # index of the ligand entry to use for computing default GRID_CENTER and OUTERBOX
LIGAND_MOLECULE = integer(default=None, min=1) # index of the ligand molecule to be removed
LIGAND_START = integer(default=1, min=1) # start ligand
LIGANDFILE = string(default='') # Glide docking ligands file name
LIGANDFILES = string_list(default=list()) # array of filenames to dock. Can be used instead of LIGANDFILE
LIGPREP = boolean(default=False) # run input ligands through LigPrep on the fly
LIGPREP_ARGS = string(default='-epik -pht 1 -s 16') # command-line options to pass to LigPrep
MACROCYCLE = boolean(default=False) # generate macrocycle ring templates on the fly using Prime
MACROCYCLE_OPTIONS = string(default='') # options string to pass to Prime's macrocycle conformer generator
MAX_ITERATIONS = integer(default=100, min=0) # maximum number of iterations during docking minimization
MAXATOMS = integer(default=500, min=1, max=500) # maximum number of ligand atoms; larger ligands will be skipped
MAXKEEP = integer(default=5000, min=1) # maximum number of poses to keep after the rough scoring stage
MAXREF = integer(default=400, min=1) # maximum number of poses to refine
MAXROTBONDS = integer(default=100, min=0, max=100) # maximum number of rotatable bonds. Ligands exceeding this limit will be skipped
METAL_CONSTRAINTS = string_list(default=list()) # METAL_CONSTRAINTS "metal1 64", ...
METAL_CUTOFF = float(default=10.0) # metal bond cutoff used for final filtering
METCOORD_CONSTRAINTS = string_list(default=list()) # METCOORD_CONSTRAINTS "label <ncoordsites>", ...
METCOORD_SITES = string_list(default=list()) # METCOORD_SITES "<x1> <y1> <z1> <r1>", "<x2> <y2> <z2> <r2>", ...; Note that the list of "<x> <y> <z> <r>" tuples in a single METCOORD_SITES specification covers *all* of the specified METCOORD_CONSTRAINTS. Thus the number of such tuples is equal to the *sum* of all the <ncoordsites> specifications.
NENHANCED_SAMPLING = integer(default=1, min=1, max=4) # expand size of the Glide funnel by N times to process poses from N confgen runs with minor perturbations to the input ligand coordinates
NMAXRMSSYM = integer(default=100, min=0) # max number of poses to compare taking symmetry into account
NOE_CONSTRAINTS = string_list(default=list()) # NOE_CONSTRAINTS "<label> <x> <y> <z> <rmin> <rmax>", ...
NOSORT = boolean(default=False) # don't sort poses from "_raw.mae" file into "_[lib|pv].mae"
NREPORT = integer(default=0, min=0) # maximum number of poses to report at the end of the job (zero means "unlimited")
NREQUIRED_CONS = string(default='ALL') # number of constraints that need to be satisfied (must be an integer or "all")
NUCLEIC_ACID_MODE = boolean(default=False) # Set to the docking mode optimized for nucleic acids
OUTERBOX = float_list(default=list(30.0, 30.0, 30.0)) # outer (grid) box size in Angstroms
PEPTIDE = boolean(default=False) # use grid and sampling settings optimized for polypeptides
PHASE_DB = string(default='') # Absolute path to Phase database to use as source of ligands to dock
PHASE_NCONFS = integer(default=1, min=1) # Number of confs per ligand to read from Phase DB
PHASE_SUBSET = string(default='') # Subset file listing the IDs of the ligands to dock from a Phase database
POSE_DISPLACEMENT = float(default=1.3, min=0.0) # minimum heavy-atom "max displacement" for counting two poses as distinct
POSE_HTORSION = float(default=40.0, min=0.0, max=60.0) # minimum deviation (degrees) in polar H torsion for counting two poses as distinct
POSE_OUTTYPE = option('poseviewer', 'ligandlib', 'poseviewer_sd', 'ligandlib_sd', 'phase_subset', 'none', default='poseviewer') # format for file containing docked poses: "poseviewer" for _pv.mae output; "ligandlib" for _lib.mae; similarly "poseviewer_sd" and "ligandlib_sd" for sdf output; "phase_subset" for bypassing _lib or _pv in favor of a Phase subset file.
POSE_RMSD = float(default=0.5, min=0.0) # minimum heavy-atom rmsd for counting two poses as distinct
POSES_PER_LIG = integer(default=1, min=1) # maximum number of poses to report per each input ligand
POSIT_CONSTRAINTS = string_list(default=list()) # POSIT_CONSTRAINTS "<label> <x> <y> <z> <r>", ...
POSTDOCK = boolean(default=True) # perform post-docking minimization and scoring
POSTDOCK_ITMAX = integer(default=500, min=1) # maximum number of iterations for post-docking minimization
POSTDOCK_NPOSE = integer(default=5) # maximum number of best-by-Emodel poses to submit to post-docking minimization
POSTDOCK_SCITMAX = integer(default=100, min=1) # maximum number of iterations for post-docking strain correction
POSTDOCKCG = boolean(default=False) # use conjugate gradient minimization (instead of variable metric) in post-docking minimization
POSTDOCKLIGMIN = boolean(default=True) # include minimization in post-docking
POSTDOCKSTRAIN = boolean(default=False) # include strain correction in post-docking score
PRECISION = option('SP', 'HTVS', default='SP') # glide docking precision
RADIUS_RES_INTERACTION = float(default=12.0, min=0.0) # use residues within this distance of the grid box center
REC_MAECHARGES = boolean(default=False) # use charges from receptor Maestro file instead of those from the force field
RECEP_CCUT = float(default=0.25, min=0.0) # charge cutoff used to determine whether to use vdW scaling of receptor atoms
RECEP_FILE = string(default=None) # receptor file name
RECEP_INDEX = integer(default=1) # index of the receptor entry in RECEP_FILE to use for gridgen (-1 means the last structure in the file)
RECEP_VSCALE = float(default=1.0, min=0.0) # vdW scaling for receptor atoms (see also RECEP_CCUT)
REF_LIGAND_FILE = string(default='') # Glide reference ligand file name
REFINDEX = integer(default=1, min=1) # index of the reference ligand structure
REPORT_CPU_TIME = boolean(default=False) # Report the CPU time spent on docking each ligand in the r_glide_cpu_time pose property
REWARD_INTRA_HBONDS = boolean(default=False) # reward formation of intramolecular hydrogen bonds in the ligand
RINGCONFCUT = float(default=2.5) # energy cutoff during ring conformer generation
RINGONFLY = boolean(default=False) # sample ring conformations if no template found and store as templates for reuse
SAMPLE_N_INVERSIONS = boolean(default=True) # include (non-ring) N inversions in confgen
SAMPLE_RINGS = boolean(default=True) # sample ring conformations using templates during confgen
SCHRODINGER_RING_TEMPLATE_SOURCES = string(default='') # Ring template file to use. Overrides the environment variable SCHRODINGER_RING_TEMPLATE_SOURCES
SCORE_INPUT_POSE = boolean(default=False) # score and report the input pose in addition to the docked poses
SCORE_MINIMIZED_INPUT_POSE = boolean(default=False) # score and report the minimized input pose in addition to the docked poses
SCORING_CUTOFF = float(default=100.0) # rough score cutoff
SHAPE_ATOMS = int_list(default=list()) # atom indexes from reference ligand that define the reference shape. Default is all heavy atoms plus polar hydrogens.
SHAPE_REF_LIGAND_FILE = string(default='') # Reference ligand for shape constraints (takes precedence over REF_LIGAND_FILE)
SHAPE_REFINDEX = integer(default=1, min=1) # index of the reference ligand structure for shape constraints
SHAPE_RESTRAIN = boolean(default=False) # apply shape constraints during docking
SHAPE_TYPING = option('ELEMENT', 'PHASE_QSAR', 'MACROMODEL', 'NONE', default='ELEMENT') # atom-typing scheme to use for shape constraints
SKIP_EPIK_METAL_ONLY = boolean(default=False) # skip ligand ionization/tautomeric states that have been prepared by Epik or LigPrep specifically to interact with a metal ion
STRAIN_GSFACTOR = float(default=0.25) # Coefficient of strain-energy correction to Glidescore
STRAIN_GSTHRESH = float(default=4.0) # Threshold for strain-energy correction to Glidescore
STRAINELEC = boolean(default=False) # include electrostatics in post-docking strain correction
USE_CONS = string_list(default=list()) # USE_CONS "<name>[:<feature_index>]", ...
USE_REF_LIGAND = boolean(default=False) # use reference ligand for RMSD evaluation or core constraints specification
USEFLEXASL = boolean(default=False) # specify movable atoms by ASL in Glide input file
USEFLEXMAE = boolean(default=False) # specify movable atoms by property in input .mae file
VSDB_MAX_HITS = integer(default=10000) # maximum hits stored in the vsdb file.
WARHEAD_ATOMS = int_list(default=list()) # the two warhead atoms in the reference ligand that are directly attached to the linker; required when using CORE_DEFINITION mcssmarts2
WRITE_CSV = boolean(default=True) # write <jobname>.csv listing results for all ligands (even ones that didn't report a pose)
WRITE_DOCKING_REPORT = boolean(default=False) # Writes out an HTML report for the docking job
WRITE_RES_INTERACTION = boolean(default=False) # generate per-residue interactions with the ligand for residues specified by "RADIUS_RES_INTERACTION" or "ASL_RES_INTERACTION"
WRITE_TIMINGS_CSV = boolean(default=False) # write a CSV file with CPU times for each subjob, as well as overall pre- and post-processing
WRITE_VSDB = boolean(default=True) # write <jobname>.vsdb listing results for the vsdb_max_hits poses.