Input Parameters

File Format

Input parameters may be supplied in a text file. There are few simple format rules for this file.

Table 2. Format of Input File

Rule

Consequence

Parameter names must be the first word on a line to be recognized.

Any character or word preceding a parameter effectively comments it out.

The word following a recognized parameter name is interpreted as the parameter value.

Comments can appear on the same line, after a parameter and value.

Blank lines are allowed.

Comments can appear on separate lines.

Empty files are allowed.

Missing parameters will be flagged (batch mode) or requested (interactive mode).

The order of parameters is irrelevant.

 

Parameters

dock has a large number of input parameters because of its wide array of functionality. Parameters are read in hierarchically, with the most general parameters first. They are also ordered according to broad classes of functionality in order to make the process of selection more intuitive. For instance all scoring-related parameters are requested together. Since only the relevant parameters are requested based on preceding selections, it is recommended that initial parameter selection be done interactively to generate a sensible input file as painlessly as possible.

The following list of parameters are grouped according to the order they are requested at run time. Again, many parameters are listed here that will not be requested during your particular run.

The default values listed here may be different from those provided during a particular run, because dock tries to recommend sensible parameter values based on preceding selections.

Table 3. dock input Parameters

3A: General 

Parameter

Type

Default

Description

Parameters in this category determine the general behavior of the dock run. Each option can be used in isolation and many in combination to allow dock to perform a diverse repertoire of tasks. If none of these flags are selected, then dock simply reads in a single molecule and writes it out, which is useful for file format conversion.

flexible_ligand

boolean

no

Flag to allow Ligand Flexibility .

orient_ligand

boolean

no

Flag to perform an Orientation Search .

score_ligand

boolean

no

Flag to perform Scoring of orientations or conformations.

minimize_ligand

boolean

no

Flag to perform local score Minimization of orientations or conformations.

multiple_ligands

boolean

no

Flag to process Multiple Ligands .

chemical_screen

boolean

no

Flag to perform Chemical Screening ( multiple_ligands must be selected, but not orient_ligand or score_ligand ).

parallel_jobs

boolean

no

Flag to perform docking as Parallel Jobs orchestrated by a server dock job ( multiple_ligands must be selected).

random_seed

integer

0

Integer to seed the random number generator.

 

3B: Ligand Flexibility 

Parameter

Type

Default

Description

Ligand flexibility parameters can be used in various combinations to relax an input conformation, to perform a conformational search of a molecule, or to perform a completely flexible docking of a molecule. See Conformation Search on page 32 for more discussion.

anchor_search

boolean

no

Flag to organize rigid segments into concentric layers around an anchor. Only the anchor is included in initial scoring/orienting. The outer segments are reattached in a subsequent conformation search.

multiple_anchors

boolean

no

Flag to select several anchors for a molecule.

  • yes = All rigid segments meeting anchor_size criteria will be tried independently as anchors.
  • no = The largest segment is used.

anchor_size

integer

10

Minimum number of heavy atoms for an anchor if multiple_anchors requested. If no segment satisfies this value, then the largest segment is used.

write_partial_structures

boolean

no

Flag to write out all partially-built structures during the anchor-first search. This option is useful to monitor the intermediate stages of a flexible ligand dock run. The structures from each cycle of growth are written to a separate file, with each file name constructed as shown in Table 6. on page 34 .

torsion_drive

boolean

no

Flag to perform a conformational search by driving each torsion through a set of low-energy dihedral values read from the flex_drive_file .

clash_overlap

real

0.5

Amount of atom VDW overlap allowed during a torsion_drive . If two ligand atoms approach closer than this fraction of the sum of the VDW radii, then the conformation is discarded. Similar to bump_overlap in grid .

  • 0 = Complete overlap allowed.
  • 1 = No overlap allowed.

configurations_per_cycle

integer

25

Sets the amount of sampling during an anchor_search with a torsion_drive . This value sets the approximate number of configurations retained during each cycle of the search. See Pruning the conformation search tree on page 36 for a full description.

conformation_cutoff_factor

integer

5

Sets the amount of sampling during a simultaneous search with a torsion_drive . This value, multiplied by the number of rotatable bonds in the molecule, sets the cutoff on the number of conformations generated, Ncut.

  • If the number of molecule conformations, N, is less than Ncut, an exhaustive systematic search of the N conformations is performed.
  • Otherwise, a random search of Ncut conformations is performed, with torsion values selected randomly from the flex_drive_file .

torsion_minimize

boolean

no

Flag to perform torsion relaxation based on intramolecular_score and/or intermolecular_score .

reminimize_layer_number

integer

2

Number of previous layers to minimize while minimizing the current segment. Only neighboring segments in inner layers (and their neighbors in outer layers) are minimized. This feature helps rescue conformations from dead ends during the search.

minimize_anchor

boolean

yes

This flag specifies whether the anchor is minimized during the initial anchor docking. In general this flag should be turned on.

reminimize_anchor

boolean

yes

If a partially-built molecule is minimized during conformation search, but no minimizable bonds are active, then a rigid-body minimization is performed. This flag will force such a rigid-body reminimization throughout the search. This method is a more expensive (but effective) way to rescue conformations.

reminimize_ligand

boolean

yes

Flag to reminimize the molecule after the conformation search, letting all torsions and the anchor position relax simultaneously. This process resolves any accumulated strain built up during the search.

flexible_bond_maximum

integer

10

The maximum number of flexible bonds allowed in a molecule, when multiple_ligands are processed.

write_conformations

boolean

no

When a conformation search is performed ( torsion_drive selected) without an orientation search, then multiple conformations may be stored with this flag. Otherwise, only the best scoring conformation is written.

write_conformation_total

integer

100

This parameter specifies the number of conformations to store per molecule.

 

3C: Orientation Search 

Parameter

Type

Default

Description

Orienting the ligand is fundamental to the docking process. Orienting is traditionally done by Matching . Alternative orienting procedures are also available, particularly the random search, which can optionally be run without any site points. For typical uses, the traditional matching process is still recommended. Please refer to Orientation Search on page 28 for more discussion.

match_receptor_sites

boolean

no

Flag to perform traditional site point-directed matching.

random_search

boolean

no

Flag to randomly search ligand orientations.

  • With match_receptor_sites , all matches are constructed randomly rather than based on distance comparisons.
  • Otherwise, orientations are randomly constructed inside the smallest rectangular volume that encloses all points read in as site points.

See Random Search on page 29 for more discussion.

ligand_centers

boolean

no

Flag to use ligand centers read in from a separate file for matching instead of ligand heavy atoms. Please refer to Macromolecular Docking on page 46 for more discussion.

automated_matching

boolean

yes (single ligand), no (multiple ligands)

Flag to let matching proceed in an automated fashion until a desired number of orientations have been formed. It is recommended for single ligand dock runs. For database searching, manual matching is recommended because dock then spends more time on ligands which are complementary to the site.

maximum_orientations

integer

5000, (500 if automated matching)

With automated_matching or random_search , this sets number of orientations to generate for each molecule. Otherwise, it sets the upper limit on the number of orientations made by matching.

write_orientations

boolean

no

When performing an orientation search with rigid ligands, this flag allows multiple orientations to be saved. Otherwise, only the best-scoring orientation of each ligand is saved.

rank_orientations

boolean

no

If multiple orientations are saved, then this flag causes orientations to be ranked by score. Otherwise, all orientations that pass a cutoff (see contact_maximum , etc) are written out in the order they are encountered.

rank_orientation_total

integer

100

Number of ranked orientations to store.

write_configurations

boolean

no

When performing an orientation search in combination with a conformation search ( torsion_drive selected), this flag allows multiple configurations (conformations + orientations) to be saved. Otherwise, only the best-scoring configuration of each ligand is saved.

write_configuration_total

integer

100

Number of configurations to store for each molecule (ranked by score).

 

3D: Matching 

Parameter

Type

Default

Description

Matching is the traditional procedure driving the orientation search in dock. If automated_matching is selected, then the amount of sampling is controlled by maximum_orientations only (and no other matching parameters can be set by the user). If it is not selected (manual matching), then the amount of sampling is controlled by the node and distance parameters. Other constraints on manual matching are available based on chemical labeling or critical clusters. See Manual Matching on page 29 for further discussion.

nodes_minimum

integer

3

Smallest number of atom-site point interactions needed to construct an orientation.

nodes_maximum

integer

10

Largest number of atom-site point interactions considered to construct an orientation

distance_tolerance

real

0.25

Maximum difference between all intra-ligand and intra-receptor distances in a match. This is the chief sampling parameter for matching.

distance_minimum

real

2.0

Minimum intra-ligand or intra-receptor distance allowed in a match. This parameter biases matching toward longer distances which convey more information about ligand or site shape.

check_degeneracy

boolean

no

Flag to discard matches that are subsets of larger matches.

reflect_ligand

boolean

no

Flag to dock the mirror image of a ligand to rescue an improper match. Half of all matches with 4 or more nodes require reflection, otherwise they are discarded. Use of this parameter is not generally recommended.

critical_points

boolean

no

Flag to force matching to include members from a particular group (or groups) of site points in every match. This parameter is useful to focus docking around a few key residues in an active site.

multiple_points

boolean

no

Flag used in combination with critical_points to allow multiple points from the same critical cluster to appear in a match.

chemical_match

boolean

no

Flag to use chemical labeling to identify bad interactions within a match so that the orientation can be discarded before it is even generated.

 

3E: Scoring 

Parameter

Type

Default

Description

Each orientation is scored according to the options selected in this section. Several scoring functions exist and are treated independently of each other. To filter molecules based on more than one function simultaneously, you will need to rescore in a subsequent step. Most scoring is speeded up by precalculating a potential on a 3D grid, but continuum scoring is available.

intramolecular_score

boolean

no

Flag to compute score between rigid segments. This feature is available if flexible_ligand is selected.

intermolecular_score

boolean

no

Flag to compute score between ligand and receptor.

gridded_score

boolean

yes

Flag to use precomputed grids to evaluate the score, otherwise a continuous evaluation is made.

grid_version

real

4

Option to select grids computed by current version of grid or by version 3.5 chemgrid.

grid_points

integer

1000000

If a version preceding 4 is selected, then this parameter specifies how many grid points are contained in the grids.

bump_filter

boolean

no

Flag to screen each orientation for clashes with receptor prior to scoring and minimizing.

bump_maximum

integer

0

Maximum number of allowed bumps.

contact_score

boolean

no

Flag to perform contact scoring.

contact_cutoff_distance

real

4.5

Interaction distance for contact scoring. Please refer to contact_cutoff_distance in grid .

contact_clash_overlap

real

0.75

Amount of VDW overlap allowed. If two atoms approach closer than this fraction of the sum of their VDW radii, then the contact score is penalized.

  • 0 = Complete overlap allowed.
  • 1 = No overlap allowed.

contact_clash_penalty

real

50

Amount that contact score is penalized for each clash.

chemical_score

boolean

no

Flag to perform chemical scoring. This feature is included for experimental purposes only. Parameterization is left to the user. Use at your own risk.

energy_score

boolean

no

Flag to perform energy scoring.

energy_cutoff_distance

real

10

Maximum distance between two atoms for their contribution to the energy score to be computed.

distance_dielectric

boolean

yes

Flag to make the dielectric depend linearly on the distance.

dielectric_factor

real

4

Coefficient of the dielectric. See Equation 1 on page 74 for context.

attractive_exponent

integer

6

Exponent of attractive Lennard-Jones term for VDW potential.

repulsive_exponent

integer

12

Exponent of repulsive Lennard-Jones term for VDW potential.

atom_model

string

u

Flag for how to model non-polar hydrogens.

  • u = United atom model. Hydrogens attached to carbons are assigned a zero VDW well-depth and the partial charge is transferred to the carbon.
  • a = All atom model. Hydrogens attached to carbons have regular VDW well-depth and partial charge is not modified.

vdw_scale

real

1

Scaling factor of vdw component of energy score.

electrostatic_scale

real

1

Scaling factor of electrostatic component of energy score.

rmsd_score

boolean

no

Flag to perform rmsd scoring, which is the rmsd of the molecules in the ligand_atom_file with respect to the molecule in the receptor_atom_file . Both molecules must have identical atoms.

contact_maximum

chemical_maximum

energy_maximum

rmsd_maximum

real

0

If orientations or ligands to be written, but not ranked, then they must pass this score cutoff to be written to file.

contact_size_penalty

chemical_size_penalty

energy_size_penalty

real

0

If ligands to be ranked, then they may be penalized by this value for each heavy atom. This helps correct for the uncomplexed score and reduce the size bias.

rmsd_override

real

0

If orientations to be written, but not ranked, then orientations with an RMSD (with respect to the input orientation) less than this value are written to file regardless of score.

 

3F: Minimization 

Parameter

Type

Default

Description

Minimization allows on-the-fly adjustment of a molecule's orientation and/or conformation to improve its score. Though this calculation is CPU intensive, it improves the efficiency of the orientation or conformation search. The simplex algorithm uses random displacements to seed the search. Consequently, minimization results vary depending on the random seed selected by the user and the order of input molecules and site points. If high-quality results are required, then repeat the run several times with different random seeds.

contact_minimize

chemical_minimize

energy_minimize

rmsd_minimize

boolean

n

Flags to perform minimization with respect to each scoring function.

initial_translation

real

1

The maximum initial step size (in Angstroms) of the simplex in each cartesian dimension. The actual step size is a random value between zero and this value.

initial_rotation

real

0.1

The maximum initial step size (unitless) for each axis of rotation. The quaternion representation is used. A value of one corresponds to a 180 degree rotation.

initial_torsion

real

10

The maximum initial step size (in degrees) for each torsion when flexible_ligand set. When several layers are minimized together, the outermost layer gets a full step and the step for each inner layer is divided by 2, 3, etc.

maximum_iterations

integer

100

Maximum number of simplex iterations for each cycle of minimization.

contact_convergence

chemical_convergence

energy_convergence

rmsd_convergence

real

0.5

Convergence criteria with respect to each scoring function. At any iteration, if all vertices of the simplex have a score within this value of the best score, then minimization terminates.

maximum_cycles

integer

1

Maximum number of minimization cycles. After the first cycle, the initial step sizes are divided by 2, 3, etc.

cycle_convergence

real

1

The distance a minimization cycle must travel to trigger another cycle. The vector distance of the final simplex vertices is used, which is normalized with respect to the initial step size.

contact_termination

chemical_termination

energy_termination

rmsd_termination

real

1

If the score is greater than this value after a cycle of minimization, then no more cycles are attempted. This parameter is useful to avoid prolonged minimization of unrecoverable orientations or conformations.

 

3G: Chemical Screening 

Parameter

Type

Default

Description

Chemical screening allows for rapid filtering of a database based on chemical and 3D distance descriptors. Before any screening can be done, the database must be keyed using the construct_screen parameter at which time Ligand Flexibility should be considered. Then screen_ligands can be activated to do pharmacophore screening or similarity screening. Make sure to use the same distance bin dimensions. See Chemical Screen on page 44 for more discussion.

construct_screen

boolean

no

Flag to construct distance chemical keys for each input molecule.

screen_ligands

boolean

no

Flag to screen input molecules based on distance chemical keys.

pharmacophore_screen

boolean

no

Flag to screen based on whether molecule keys include pharmacophore pattern.

similarity_screen

boolean

no

Flag to screen based on similarity of molecule keys to target keys.

dissimilarity_maximum

float

0.25

Maximum dissimilarity with target to write out molecule.

distance_begin

float

2

Smallest distance of interest in fingerprint.

distance_end

float

17

Largest distance of interest in fingerprint.

distance_interval

float

0.5

Distance resolution of fingerprint. The total number of distance keys cannot exceed 30, since a 32-bit key is currently used with the terminal bits being reserved for out-of-range values.

 

3H: Parallel Jobs 

Parameter

Type

Default

Description

The parallel job parameters provide a convenient way to process a large database of molecules and distribute the workload over many computers. One dock job must be configured as a server job. Any number of other jobs running on separate machines are configured as client jobs. The server job reads the entire database and parses molecules out to the client jobs for processing. It is recommended that the server job be executed on the computer which stores the database. The server job and each client job requires its own input file. See Database Processing on page 42 for more discussion.

parallel_server

boolean

no

Flag to identify this job as the server job.

server_name

string

server

The name used by the server job to communicate with client jobs.

client_total

integer

5

The number of client jobs at the disposal of this server job.

client_name_1

client_name_2

client_name_3 ...

string

clientN

If parallel_server set, then this list of names of client jobs is requested.

client_name

string

client

If parallel_server not set, then the name of this particular client job is requested. To be recognized by the server, this name must be included in the client_name_N list supplied to the server job.

 

3I: Multiple Ligands 

Parameter

Type

Default

Description

The parameters in this category control the processing of a database of ligands. See Database Processing on page 42 for more discussion.

ligands_maximum

integer

1000

The maximum number of ligands to read in from the input file. This INCLUDES skipped ligands.

initial_skip

integer

0

The initial number of ligands to skip. This is useful to position the reading stream to a particular point in the input file.

interval_skip

integer

0

The number of ligands to skip for every ligand processed. This is useful to perform a preliminary scan a database for timing purposes, or to coordinate the processing of a database over multiple machines.

heavy_atoms_minimum

integer

0

Minimum number of heavy atoms. In general, set this to at least three (or nodes_minimum ) when an Orientation Search is performed.

heavy_atoms_maximum

integer

100

Maximum number of heavy atoms.

rank_ligands

boolean

no

Flag to rank best molecules.

  • yes = Only top scorers written.
  • no =For each molecule, the best orientation (or set of orientations with write_orientations ) is written.

rank_ligand_total

integer

100

Number of ranked ligands.

restart_interval

integer

100

Number of ligands to process between each time restart information is saved.

 

3J: Input 

Parameter

Default

Description

The user must supply several kinds of input files.

  • Coordinate Contains molecules/site points (*.mol2, *.pdb, *.xpdb, *.ptr, *.sph).
  • Grid Contains precalculated score potentials (*.bmp, *.cnt, *.chm, *.nrg).
  • Parameter Contains VDW, chemical and flexibility parameters (*.defn, *.tbl).
  • Control Empty. Used to interact with a running job (*.quit, *.dump).

ligand_atom_file

ligand.mol2

File containing ligand atom coordinates.

ligand_center_file

ligand_center.sph

File containing ligand site points (see Macromolecular Docking on page 46 ).

receptor_site_file

receptor_site.sph

File containing receptor site points.

score_grid_prefix

score_grid

Prefix for files containing precalculated score grids.

receptor_atom_file

receptor.mol2

File containing receptor atom coordinates. Used for continuum (no grids) scoring when gridded_score not set.

vdw_definition_file

$PATH/vdw.defn

File containing VDW labels and parameters. See vdw.defn on page 105 .

chemical_definition_file

$PATH/chem.defn

File containing chemical labels and definitions. See chem.defn on page 106 .

chemical_match_file

$PATH/chem_match.tbl

File containing chemical interaction table for use when chemical_match set. See chem_match.tbl on page 107 .

chemical_score_file

$PATH/chem_score.tbl

File containing chemical interaction table for use when chemical_score set. See chem_score.tbl on page 108 .

chemical_screen_file

$PATH/chem_screen.tbl

File containing chemical interaction table for use when similarity_screen set. See chem_screen.tbl on page 109 .

flex_definition_file

$PATH/flex.defn

File containing flexible bond labels and definitions for use when flexible_ligand set. See flex.defn on page 110 .

flex_drive_file

$PATH/flex_drive.tbl

File containing torsion parameters for a torsion_drive search. See flex_drive.tbl on page 111 .

quit_file

*.quit

When multiple_ligands is set, this file may be created by the user at any time to signal the dock job to terminate execution. If rank_ligands is set, the best molecules are written to file and an up-to-date restart file is generated.

dump_file

*.dump

If rank_ligands is set, this file may be created by the user at any time to signal the dock job to write the best molecules to file and resume execution.

 

3K: Output 

Parameter

Default

Description

dock writes up to three kinds of output files.

  • Coordinate Contains docked molecules (*.mol2, *.pdb, *.xpdb, *.ptr, *.sph).
  • Info Contains current ligand rankings.
  • Restart Contains restart information.

ligand_out_file

ligand_contact_file

ligand_chemical_file

ligand_energy_file

ligand_rmsd_file

ligand_out.mol2

ligand_cnt.mol2

ligand_chm.mol2

ligand_nrg.mol2

ligand_rms.mol2

Files containing docked, minimized, rescored, or reformatted molecules for each type of scoring.

info_file

*.info

File containing summary information about the current rank_ligands list.

restart_file

*.rst

File containing detailed information about current rank_ligands list which is sufficient for restarting if the current job is prematurely terminated. See Command-line Arguments on page 53 for restart instructions.

 

UC Regents 1998
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