The glide Command

The glide command is used for both receptor grid generation and ligand docking jobs. For ligand docking, it can run both single processor and distributed docking jobs. The syntax of the command is as follows:

glide [options] input-file

For a description of the command options, run the command glide -h.

The input file is a Glide input file, whose default extension is .in. This file contains keyword-value pairs that define the parameters of the calculation. These keywords are listed in the tables below. Table 1 contains keywords for grid generation jobs, and Table 2 contains keywords for ligand docking jobs. The keywords for grid generation and ligand docking are grouped according to the tabs (and associated Advanced Settings dialog boxes) in the Receptor Grid Generation and Ligand Docking panels in which they are set. Defaults are available for many of the keywords, so you do not need to include all the keywords in the input file.

Boolean values in the input file can be represented by True or False, Yes or No, 1 or 0. The last two pairs are converted internally to True or False. The values are case-insensitive. A Boolean value is denoted by boolean in the tables below, and the value is represented by True or False, which you can change as you will.

Table 1. Glide input file keywords for grid generation jobs
Keyword	Description
`GRIDFILE` filename	Filename of the grid `.zip` file, if compressed, or the `.grd` file.
`CV_CUTOFF` value	Coulomb-van der Waals cutoff.
`FORCEFIELD {OPLS4\| OPLS2005}`	Specify the force field to use. The default is `OPLS2005`.
Receptor keywords
`RECEP_FILE` filename	Receptor file name. Must be a Maestro file (`.mae`, `.maegz`, `.mae.gz`). The receptor must be the first entry in this file. If `LIGAND_MOLECULE` is used, the receptor entry must contain the ligand as well, which is removed for the grid generation. If `LIGAND_INDEX` is used, the ligand must be a separate entry in the file.
`RECEP_VSCALE` value	General van der Waals radius scaling factor. Default: 1.0.
`RECEP_CCUT` value	General van der Waals radius scaling partial charge cutoff. Default: 0.25.
`GLIDE_RECEP_MAESCALE` boolean	Read per-atom scale factors from the input structure file if set to `True`. Default: `False`.
`GLIDE_RECEP_ASLSCALE` boolean	Specify per-atom scale factors by ASL if set to `True`. Default: `False`.
`ASLSTRINGS` list	Comma-separated list of quoted ASL expressions, one expression for each set of residues to be scaled. Only used if `GLIDE_RECEP_ASLSCALE` is set to `True`.
`GLIDERECEPTORSCALECHARGES` list	Comma-separated list of charge scaling factors, one factor for each set of residues that is defined in the `ASLSTRINGS` list.
`GLIDERECEPTORSCALERADII` list	Comma-separated list of van der Waals scaling factors, one factor for each set of residues that is defined in the `ASLSTRINGS` list.
`REC_MAECHARGES` boolean	Use partial charges from the input structure if set to `True`. Default: `False`.
`HBOND_ACCEP_HALO` boolean	Accept halogens (neutral or charged, F, Cl, Br, or I) as H-bond acceptors. Default: `False`.
`HBOND_DONOR_HALO` boolean	Accept the halogens (Cl, Br, I, but not F) as potential “H-bond” (noncovalent interaction) donors. Default: `False`.
`HBOND_DONOR_AROMH` boolean	Accept aromatic hydrogens as potential H-bond donors. Default: `False`.
`HBOND_DONOR_AROMH_CHARGE` value	Partial charge cutoff for accepting aromatic hydrogens as potential H-bond donors. The cutoff is applied to the actual (signed) charge, not the absolute value. Default: 0.0.
`PEPTIDE` boolean	Set up grids for peptide docking. Required if peptides are to be docked.
Site keywords
`INNERBOX` x`,`y`,`z	Comma-separated list of the x, y, and z dimensions of the inner (ligand centroid bounding) box in angstroms. These values must be integers. Written to the receptor Maestro file as `r_glide_gridbox_lig`q`range`, where q is `x`, `y`, or `z`.
`ACTXRANGE` value	Outer box x dimension. Must be set to the same as for the `OUTERBOX` keyword.
`ACTYRANGE` value	Outer box y dimension. Must be set to the same as for the `OUTERBOX` keyword.
`ACTZRANGE` value	Outer box z dimension. Must be set to the same as for the `OUTERBOX` keyword.
`OUTERBOX` x`,`y`,`z	Comma-separated list of the x, y, and z dimensions of the outer (grid) box in angstroms. These values can be floating-point numbers. Written to the receptor Maestro file as `r_glide_gridbox_`q`range`, where q is `x`, `y`, or `z`.
`GRID_CENTER` x`,`y`,`z	Comma-separated list of the x, y, and z coordinates of the center of the grid. These values can be floating-point numbers. Written to the receptor Maestro file as `r_glide_gridbox_`q`cent`, where q is `x`, `y`, or `z`.
`GRID_CENTER_ASL` asl	Specify the grid center with the ASL expression asl. The center is placed at the centroid of the atoms defined in the ASL expression.
`LIGAND_MOLECULE` number	Specify the molecule number of the ligand that defines the grid center.The center is placed at the centroid of the ligand atoms. If this keyword is used, the receptor entry in the file must contain the ligand, which is removed for the grid generation.
`LIGAND_INDEX` number	Specify the index of the ligand in the receptor file that defines the grid center. The center is placed at the centroid of the ligand atoms. If this keyword is used, the receptor file must contain the ligand as a separate entry (e.g. in a pose-viewer type file), and the receptor must be the first entry.
Constraints keywords
`GLIDECONS` boolean	Define constraints if set to `True`. Default: `False`.
`GLIDE_NTOTALCONS` ncons	Total number of constraints defined (Positional/NOE+H-bond/Metal+Hydrophobic+Metal Coordination).
`GLIDE_NUMPHOBCONS` nhpc	Number of hydrophobic constraints defined.
`GLIDE_NUMPOSITCONS` npc	Number of positional constraints defined.
`GLIDECONSATOMS` list	Comma-separated list of atom numbers that define H-bond/Metal constraints.
`GLIDECONSNAMES` list	Comma-separated list of constraint names.
`GLIDECONSUSESYMATOMS` list	Include symmetry-related atoms when applying constraints. List of Booleans for each H-bond or metal constraint, which matches the list given for `GLIDECONSATOMS`. Default: `True` for all H-bond and metal constraints.
`GLIDE_NUMMETCOORDCONS` value	Number of metal-coordination constraints (number of metals selected for coordination constraints).
`GLIDE_NUMMETCOORDSITES` list	List of the number of available coordination sites for each metal coordination constraint.
`GLIDE_CONS_XMETCOORD` list `GLIDE_CONS_YMETCOORD` list `GLIDE_CONS_ZMETCOORD` list	Comma-separated list of coordinates of the metal coordination sites. The coordinates of the sites for each metal center should be contiguous, and they should be in the order implied by the list defined by `GLIDE_NUMMETCOORDSITES`.
`GLIDE_CONS_RMETCOORD` list	Comma-separated list of radii of the metal coordination spheres, which represent the maximum allowed distance of a ligand atom from the coordination site.
Rotatable groups keywords
`USEFLEXMAE` boolean	Include flexible groups in the grid generation, as specified in the Maestro file for the receptor. Only one of `USEFLEXMAE` and `USEFLEXASL` can have the value `True`.
`USEFLEXASL` boolean	Include flexible groups in the grid generation, as specified by the `FLEXASL` keyword. Only one of `USEFLEXMAE` and `USEFLEXASL` can have the value `True`.
`FLEXASL` asl	ASL expression that specifies the hydrogens on the flexible groups. The expression must specify only the required hydroxyl and thiol hydrogens.
Excluded volumes keywords
`GLIDE_NUMEXVOL` value	Number of excluded volumes. For each excluded volume, the coordinates of the center and the radius must be defined, at a minimum.
`GLIDE_XEXVOL` list `GLIDE_YEXVOL` list `GLIDE_ZEXVOL` list	Comma-separated list of coordinates of the centers of the excluded volume spheres.
`GLIDE_REXVOL` list	Comma-separated list of radii of the excluded volume spheres.
`GLIDEXVOLNAMES` list	Comma-separated list of names of the excluded volumes.
`GLIDE_REXVOLIN` list	Comma-separated list of the inner radii of the excluded volume spheres (the radii at which the penalties have their full values). Default is 90% of the sphere radius.

Keyword

Description

GRIDFILE filename

File name of the grid .zip file, if compressed, or the .grd file.

Settings keywords

DOCKING_METHOD {confgen|rigid| mininplace|inplace}

Docking method:

`confgen`	Dock flexibly.
`rigid`	Dock rigidly.
`mininplace`	Refine (do not dock)
`inplace`	Score in place (do not dock)

PRECISION {XP|SP|HTVS}

Docking precision mode. Set in the Settings tab.

CANONICALIZE boolean

Canonicalize the input structure by discarding the coordinates and regenerating the structure from the connectivity and stereochemistry. Takes about 1 sec per ligand. Default: True.

LIGPREP boolean

Run LigPrep on the input structures as they are processed, using the LigPrep libraries. Not supported with Phase databases as input.

Default: True for SMILES and CSV input files, False otherwise.

LIGPREP_ARGS list

Specify options for LigPrep, as a string containing the options as they would be given with the ligprep command. The string must be in quotes if it contains commas.
Default: -epik -pht 1 -s 16.

SAMPLE_N_INVERSIONS boolean

Sample nitrogen inversions if set to True and DOCKING_METHOD is set to confgen. Default: True.

SAMPLE_RINGS boolean

Sample rings if set to True and DOCKING_METHOD is set to confgen. Default: True.

INCLUDE_INPUT_RINGS boolean

Include the input structure along with any generated ring conformations. Only applies if SAMPLE_RINGS is set to True (otherwise the input structure is the only structure). Default: False.

MACROCYCLE boolean

Perform sampling of macrocycles if set to True. Only macrocycles are docked: non-macrocycles are skipped. Default: False.

RINGONFLY boolean

Generate templates dynamically for unrecognized rings of up to 14 atoms. Only available with OPLS_2005. Default: False.

AMIDE_MODE {penal|free| fixed|trans|gen}

Amide bond sampling mode. Only set when DOCKING_METHOD is set to confgen. Default: gen.

`penal`	penalize nonplanar conformation
`free`	vary conformation
`fixed`	retain original conformation
`trans`	allow trans conformation only
`gen[eralized]`	use generalized torsion controls defined in `torcontrol.txt`.

AMIDE_TRANSTOL angle

Maximum angle deviation in degrees from 180° for an amide to be considered trans. Default: 20.

EPIK_PENALTIES boolean

Apply penalties for ionization or tautomeric states calculated by Epik. Default: True.

SKIP_EPIK_METAL_ONLY boolean

Skip Epik-generated states of ligands that are designed for binding to metals. This option is useful if the receptor has a metal but the ligand does not bind to it. These states are skipped by default if the receptor does not have a metal.

EXPANDED_SAMPLING boolean

Expand the sampling by bypassing the elimination of poses in the rough scoring stage. Useful for fragment docking. Default: False.

REWARD_INTRA_HBONDS boolean

Reward intramolecular ligand hydrogen bonds by adding a contribution for each intramolecular hydrogen bond to the GlideScore, and a contribution to Emodel. Default: False.

HBOND_DONOR_AROMH boolean

Accept aromatic hydrogens as potential H-bond donors. Default: False.

HBOND_DONOR_AROMH_CHARGE value

Partial charge cutoff for accepting aromatic hydrogens as potential H-bond donors. The cutoff is applied to the actual (signed) charge, not the absolute value. Default: 0.0.

HBOND_ACCEP_HALO boolean

Accept halogens (neutral or charged, F, Cl, Br, or I) as H-bond acceptors. Default: False.

HBOND_DONOR_HALO boolean

Accept the halogens (Cl, Br, I, but not F) as potential “H-bond” (noncovalent interaction) donors. Default: False.

GLIDEUSEALLEXVOL boolean

Apply all excluded volumes that are included with the grid.

GLIDE_EXVOL_PENAL_STRENGTH value

Set the strength of the penalty for occupying an excluded volume. Allowed values: large, medium, small. These values are translated into a numeric value for each volume. Default: large.

GLIDE_NUMUSEXVOL value

Number of excluded volumes to use in docking. Must not be greater than the total number, specified by GLIDE_NUMEXVOL. for grid generation.

GLIDEUSEXVOLNAMES list

Comma-separated list of names of the excluded volumes to use in docking.

GLIDE_EXVOL_PENAL_NUM list

Comma-separated list of maximum penalty values for each excluded volume used in docking.

WRITE_XP_DESC boolean

Write XP descriptor information if set to True. Default: False.

FLEXTORS boolean

Set to False for rigid, refineinput and inplace jobs.

MAXKEEP nposes

Number of poses per ligand to keep in initial phase of docking. Default: 5000.

SCORING_CUTOFF cutoff

Scoring window for keeping initial poses. Default: 100.0.

MAXREF nposes

Number of poses to keep per ligand for energy minimization. Maestro sets this number to 800 for XP. Default: 400.

GLIDE_DIELCO constant

Distance-dependent dielectric constant. Default: 2.0.

FORCEFIELD {OPLS4| OPLS2005}

Specify the force field to use. Default: OPLS2005.

FORCEPLANAR boolean

Scale force-field parameters for planar (sp²) systems such as rings to strongly penalize nonplanar conformations. Default: False.

MAX_ITERATIONS niter

Maximum number of conjugate gradient steps. Default:100.

PEPTIDE boolean

Set parameters for improving docking results for polypeptides. The following settings are made if the keywords are not already set:

`MAXKEEP`	100000
`MAXREF`	1000
`POSTDOCK_NPOSE`	100

Other keywords are set internally: the maximum number of conformers is increased by a factor of 10, and the number of diameter directions is increased by about a factor of 3.

It is recommended to follow docking with Prime MM-GBSA postprocessing, for minimization of the peptide and for scoring.

Not available for HTVS docking precision.

Ligands keywords

GLIDECONSUSEMET boolean

Use individual metal and ligand radii to determine the cutoff for metal-ligand constraints (r_metal+r_ligand+0.4), rather than a single global value of 2.4 Å. Default: False.

GLIDESCORUSEMET boolean

Use individual metal radii for the cutoff in the scoring function, rather than a single ramp from 2.2 to 2.6 Å. Default: False.

LIGANDFILE filenames

Comma-separated list of ligand file names. File names that include commas can be quoted; leading and trailing spaces are ignored. Files can be in any of Maestro, SD, MOL2, or PDB format.If LIGAND_START and LIGAND_END are used, they refer to the ligand indices as if the input files were concatenated in the order specified.

LIGAND_START firstlig

First ligand from the ligand file to be docked. Default: 1.

LIGAND_END lastlig

Last ligand from the ligand file to be docked. Default: last in file.

PHASE_DB dbpath

Full path to Phase database to use for the ligands. The first conformer of each ligand is extracted from the database for docking. Use instead of LIGANDFILE, LIGAND_START, LIGAND_END.

PHASE_SUBSET filename

Name of subset file to use in the Phase database. Only the ligands whose records are listed in the subset file are docked. If omitted, all ligands in the database are docked.

PHASE_NCONFS n

Number of conformers to dock for each ligand from the Phase database. Each conformer is docked separately. The n lowest-energy conformers are taken for each ligand. When using this keyword, canonicalization is disabled.

LIG_MAECHARGES boolean

Take charges from input structures if set to True. Default: False.

MAXATOMS maxatoms

Maximum number of atoms per ligand.
Default (and maximum): 500.

MAXROTBONDS maxrotbonds

Maximum number of rotatable bonds per ligand.
Default (and maximum): 100

LIG_VSCALE factor

Scaling factor for van der Waals radii scaling. Default: 0.8.

LIG_CCUT cutoff

Partial charge cutoff for van der Waals radii scaling. Default: 0.15.

RINGCONFCUT cutoff

Energy window for retention of ring conformers. Default: 2.5 kcal mol^-1.

Core keywords

USE_REF_LIGAND boolean

Use core pattern for comparison or restraint if set to True. Default: False.

REF_LIGAND_FILE filename

File name for reference ligand. File format can be Maestro, SD, MOL2 or PDB.

CORE_DEFINITION {all| allheavy|smarts|mcssmarts}

Specify how the core is defined. Default: allheavy.

`all`	use all atoms in the reference ligand
`allheavy`	use all nonhydrogen atoms in the reference ligand
`smarts`	use the SMARTS pattern defined by the `CORE_ATOMS` keyword. When used without `CORE_ATOMS`, the constraints will be automatically determined based on the `smarts` as long as the SMARTS pattern has a unique match.
`mcssmarts`	use the MCS of the reference ligand and the current ligand.

CORE_ATOMS list

List of core atoms to use for the RMSD calculation. Ranges for input atom indexes are allowed. Only set when CORE_DEFINITION is set to smarts. Now optional for jobs using CORE_DEFINITION smarts as long as the SMARTS pattern matches the reference ligand exactly once. In this case, all atoms matched by the SMARTS pattern are used as core atoms.

CORE_SMARTS pattern

Smarts pattern for core. Only set when CORE_DEFINITION is set to smarts. Set in the Core tab.

CORE_RESTRAIN boolean

Restrict docking to reference position if set to True. Default: False.

CORE_SNAP boolean

When using core constraints, “snap” the core of the ligand to exactly match the reference ligand and rebuild the rest of the ligand with the new core, if set to True. If set to False, use the filter-and-restrain approach.

Not compatible with CORE_DEFINITION all.

Default: True if CORE_POS_MAX_RMSD < 0.75, False otherwise.

CORE_POS_MAX_RMSD value

Tolerance on the RMSD to use when restricting docking to the reference position.

CORE_FILTER boolean

Skip ligands that do not match the core pattern if set to True. Default: False.

CORECONS_FALLBACK boolean

Fall back to the filter-and-restrain approach when docking produces no poses with CORE_SNAP set to True. Default: False.

Constraints keywords

[FEATURE:n]

Define a feature block. A feature is use to define the ligand atoms that match a given constraint, and is defined by a set of SMARTS patterns and rules. The feature block consists of one or more PATTERN lines. The index n is used to associate the feature with a constraint specified by USE_CONS. The square brackets must be included.

PATTERNistring

Define a ligand matching pattern in a feature block. The index i must be unique within a block. The string consists of the following components, separated by spaces:

1. SMARTS pattern.

2. Comma-separated list of atoms in the SMARTS pattern that must be matched by the ligand.

3. Optional keyword include or exclude, for including or excluding matched atoms. Default is include. exclude can only be used to limit the scope of an included pattern.

4. For hydrophobic constraints, number of atoms required in the constraint region. Must be preceded by include.

[CONSTRAINT_GROUP:m]

Define a constraint group. Must be followed by a USE_CONS keyword and a NREQUIRED_CONS keyword. The square brackets must be included. All constraints must be defined as part of a group. The ligand must satisfy the constraints in each group.

USE_CONS list

Apply the specified constraints as part of the constraint group. The list is a comma-separated list of constraints. Each constraint is specified in the format title[:n], where title is the label of the constraint in the .cons file for the grid, and n, if it is supplied, must match the index of a FEATURE block. If n is not given, the default features are used.

NREQUIRED_CONS nreq

Number of constraints in the USE_CONS list that are required to match. The sum of nreq values over all constraint groups must not exceed 4.

GLIDE_CONS_FINALONLY boolean

Test constraint satisfaction only after docking if set to True. Default: False.

HAVEGLIDECONSFEAT boolean

Deprecated, but retained for backward compatibility. A feature file is already available if set to True. Default: False.

GLIDECONS boolean

Deprecated, but retained for backward compatibility. Use constraints if set to True. Default: False.

GLIDE_CONS_FEAT_FILE filename

Deprecated, but retained for backward compatibility. Specify the name of the constraints feature file. Default: jobname.feat.

GLIDEUSECONSFEAT boolean

Deprecated, but retained for backward compatibility. Use the constraints feature file for the application of constraints if set to True. If set to False, the constraint information is in the Impact .inp file.

Torsional constraints keywords

[TORCONS:index]

Define a torsional constraint block. If a torsion matches a constraint definition in more than one block, the match in the block with the highest index. is used. These blocks must be contiguous and be placed at the end of the input file.

SMARTS "pattern"

Define part of a molecule in which torsional constraints can be defined by the specified SMARTS pattern. The pattern must be enclosed in quotes.

ATOMS list

Define torsions to be constrained. The list of atoms that define the torsions is a comma-separated list of quoted atom number quartets. The atom numbers are separated by hyphens. For example:

ATOMS "1-2-3-4","2-3-4-5","4-5-6-7"

The atom numbering is given relative to the SMARTS pattern.

USEVAL list

Specify which torsions should be set to the corresponding values given in the list for the TORVAL keyword. The list is a comma-separated list of integer values. The default is 0 for all values, which means that the input value of the torsion will be used.

TORVAL values

Specify the angle values to which the torsions should be set before constraining them, if the corresponding boolean value in the USEVAL list is True. The angle values are a comma-separated list.

ALLBONDS boolean

Constrain torsions about all bonds for which a dihedral (defined by four atoms) is fully contained in the SMARTS pattern, using the value for each torsion from the input structure. Any ATOMS, SETVAL, and TORVAL keywords in the constraint block are ignored.

Output keywords

COMPRESS_POSES {TRUE|FALSE}

Compress the output pose files. Default: TRUE.

NOSORT {TRUE|FALSE}

Do not sort the poses by score (using glide_sort), but return the poses as generated in jobname_raw.maegz.

CV_CUTOFF cutoff

Reject poses with Coulomb-van der Waals energy greater than cutoff kcal/mol. Default: 0.0.

HBOND_CUTOFF cutoff

Reject poses with H-bond score greater than cutoff. Default: 0.0.

METAL_CUTOFF cutoff

Reject poses with metal score greater than cutoff. Default: 10.0.

POSE_OUTTYPE {poseviewer|ligandlib| poseviewer_sd|ligandlib_sd| phase_subset|none}

Type of output file to produce. Default: poseviewer.

`poseviewer`	Write pose viewer file (`_pv.maegz`); includes receptor as first structure.
`poseviewer_sd`	Write pose viewer file in SD format (`_pv.sdfgz`); receptor stored in V3000 format.
`ligandlib`	Write ligand pose file (`_lib.maegz`); does not contain receptor.
`ligandlib_sd`	Write ligand pose file in SD format (`_lib.sdfgz`).
`phase_subset`	Write a Phase subset file (`_phase.inp`). This option can only be used when screening a Phase database (`PHASE_DB`).
`none`	Do not write any kind of ligand pose file. Pose writing is skipped entirely. This option is useful if you only want the scores.

SD format is not available with flexible groups in the grid or with XP descriptors.

WRITE_CSV boolean Write a CSV file that contains a selection of properties for all ligands in the input file. The properties include the ligand number and a status column with values DOCKED, SKIPPED, and DIED. No other properties are reported for ligands that died (failed); the title is given for skipped ligands, and properties such as the scores are given for ligands that were docked successfully.

POSE_RMSD

RMS deviation used in clustering to discard poses, in angstroms. Default: 0.5.

POSE_DISPLACEMENT

Maximum atomic displacement used in clustering to discard poses, in angstroms. Default: 1.3.

NMAXRMSSYM

Maximum number of poses to compare taking local symmetry into account, when detecting duplicates. A negative value means that there is no limit. Default: 100.

NREPORT maxposes

Maximum number of poses to write out from the docking run. Default: 0, meaning write out all poses.

POSES_PER_LIG maxperlig

Maximum number of poses to write per ligand. Default: 1.

POSTDOCK boolean

Use post docking minimization if set to True. Default: True.

POSTDOCK_NPOSE npose

Number of poses to use in post-docking minimization. Maestro sets this number to 10 for XP. Default: 5.

POSTDOCKSTRAIN boolean

Apply strain correction terms if set to True. Default: False.

WRITE_RES_INTERACTION boolean

Generate per-residue interaction terms if set to True. Default: False.

WRITE_VSDB boolean

Generate a .vsdb file when running a distributed Glide job, containing all the poses from the output of the run. Default: True.

VSDB_MAX_HITS cutoff

Specify a value of up to 50,000 for the cutoff number of screening hits which the generated .vsdb file will contain. Default: 10_000

ASL_RES_INTERACTION asl

ASL expression defining residues to be used for per-residue interactions. Takes precedence over RADIUS_RES_INTERACTION.

RADIUS_RES_INTERACTION r

Radius for per-residue interaction terms, in angstroms. Only set if WRITE_RES_INTERACTION is set to True. Default: 12.0

KEEPSKIPPED boolean

Write a file jobname_skipped.maegz containing the ligands that were skipped or rejected at any point in the docking process. Default: False.

KEEP_SUBJOB_POSES boolean

Keep the zip archive, jobname_subjob_poses.zip, and copy it back to the job launch directory. This archive contains the pose files from all the subjobs of a distributed docking job. Default: True.

CALC_INPUT_RMS boolean

Calculate RMSD between each pose and its input structure. Default: False.