Rigid body docking sampling module
Module contents
Rigid-body docking sampling module
This module does a randomization of orientations and rigid-body
minimization. It corresponds to the classical it0 step in the HADDOCK2.x
series.
In this module, the interacting partners are treated as rigid bodies, meaning that all geometrical parameters such as bond lengths, bond angles, and dihedral angles are frozen. The partners are first separated in space and randomly rotated around their respective centres of mass. Afterwards, the molecules are brought together by rigid-body energy minimisation with rotations and translation as the only degrees of freedom.
The driving force for this energy minimisation is the energy function, which consists of the intermolecular van der Waals and electrostatic energy terms and the restraints defined to guide the docking. The restraints are distance-based and can consist of unambiguous or ambiguous interactions restraints (AIRS). In ab-initio docking mode those restraints can be automatically defined in various ways; e.g. between center of masses (CM restraints) or between randomly selected patches on the surface (random AIRs).
The definition of those restraints is particularly important as they effectively guide the minimisation process. For example, with a stringent set of AIRs or unambiguous distance restraints, the solutions of the minimisation will converge much better and the sampling can be limited. In ab-initio mode, however, very diverse solutions will be obtained and the sampling should be increased to make sure to sample enough the possible interaction space.
- class haddock.modules.sampling.rigidbody.HaddockModule(order: int, path: Path, initial_params: str | Path = PosixPath('/opt/hostedtoolcache/Python/3.10.15/x64/lib/python3.10/site-packages/haddock/modules/sampling/rigidbody/defaults.yaml'))[source]
Bases:
BaseCNSModuleHADDOCK3 module for rigid body sampling.
- make_cns_jobs(inp_list: Sequence[tuple[list[PDBFile], Path | str, str | None, int]]) list[CNSJob][source]
Default Parameters
Easy
ambig_fname
default: ‘’
type: file
title: Ambiguous distance restraints filename
short description: Filename of the ambiguous distance restraints file
long description: Filename of the ambiguous distance restraints file. By default 50% of those restraints will be randomly discared. This can be changed/turned off and is controlled by the randremoval and npart parameters. Note that this file can contain both ambiguous and unambiguous restraints.
group: distance restraints
explevel: easy
elecflag
default: True
type: boolean
title: Include electrostatics energy
short description: Include electrostatics energy during the calculations.
long description: Include electrostatics energy during the calculations. If set to false electrostatics will not be considered.
group: force field
explevel: easy
hbond_fname
default: ‘’
type: file
title: H-bond restraints filename
short description: Filename of the hydrogen bond distance restraints file
long description: Filename of the hydrogen bond distance restraints file. Note that this file can contain any type of distance restraints.
group: distance restraints
explevel: easy
mol_shape_1
default: False
type: boolean
title: Is the molecule a shape?
short description: Defines a molecule as a shape.
long description: Defines a molecule as a shape, which is a collection of beads.
group: molecule
explevel: easy
randorien
default: True
type: boolean
title: No title yet
short description: No short description yet
long description: No long description yet
group: sampling
explevel: easy
sampling
default: 1000
type: integer
title: Number of models to generate
min: 1
max: 50000
short description: Number of rigidbody docking models to generate
long description: Number of rigidbody docking models to generate
group: sampling
explevel: easy
unambig_fname
default: ‘’
type: file
title: Unambiguous restraints filename
short description: Filename of the unambiguous distance restraints file
long description: Filename of the unambiguous distance restraints file. All restraints in that file will be used. Note that this file can contain both ambiguous and unambiguous restraints.
group: distance restraints
explevel: easy
Expert
ambig_scale
default: 50
type: integer
title: Force constant for ambiguous distance restraints
min: 0
max: 1000
short description: Force constant applied to the distance restraints defined in ambig_fname.
long description: Force constant applied to the distance restraints defined in ambig_fname.
group: distance restraints
explevel: expert
c2sym_end1_1
default: nan
type: integer
title: Residue number of last residue
min: -9999
max: 9999
short description: Residue number of last residue in the first C2 symmetry segment
long description: Residue number of last residue in the first C2 symmetry segment
group: symmetry
explevel: expert
c2sym_end2_1
default: nan
type: integer
title: Residue number of last residue
min: -9999
max: 9999
short description: Residue number of last residue in the second C2 symmetry segment
long description: Residue number of last residue in the second C2 symmetry segment
group: symmetry
explevel: expert
c2sym_seg1_1
default: ‘’
type: string
title: Segment ID of first C2 segment
short description: Segment ID of first C2 segment
long description: Segment ID of first C2 segment
group: symmetry
explevel: expert
c2sym_seg2_1
default: ‘’
type: string
title: Segment ID of second C2 segment
short description: Segment ID of second C2 segment
long description: Segment ID of second C2 segment
group: symmetry
explevel: expert
c2sym_sta1_1
default: nan
type: integer
title: Residue number of first residue
min: -9999
max: 9999
short description: Residue number of first residue in the first C2 symmetry segment
long description: Residue number of first residue in the first C2 symmetry segment
group: symmetry
explevel: expert
c2sym_sta2_1
default: nan
type: integer
title: Residue number of first residue
min: -9999
max: 9999
short description: Residue number of first residue in the second C2 symmetry segment
long description: Residue number of first residue in the second C2 symmetry segment
group: symmetry
explevel: expert
c3sym_end1_1
default: nan
type: integer
title: Residue number of last residue
min: -9999
max: 9999
short description: Residue number of last residue in the first C3 symmetry segment
long description: Residue number of last residue in the first C3 symmetry segment
group: symmetry
explevel: expert
c3sym_end2_1
default: nan
type: integer
title: Residue number of last residue
min: -9999
max: 9999
short description: Residue number of last residue in the second C3 symmetry segment
long description: Residue number of last residue in the second C3 symmetry segment
group: symmetry
explevel: expert
c3sym_end3_1
default: nan
type: integer
title: Residue number of last residue
min: -9999
max: 9999
short description: Residue number of last residue in the third C3 symmetry segment
long description: Residue number of last residue in the third C3 symmetry segment
group: symmetry
explevel: expert
c3sym_seg1_1
default: ‘’
type: string
title: Segment ID of first C3 segment
short description: Segment ID of first C3 segment
long description: Segment ID of first C3 segment
group: symmetry
explevel: expert
c3sym_seg2_1
default: ‘’
type: string
title: Segment ID of second C3 segment
short description: Segment ID of second C3 segment
long description: Segment ID of second C3 segment
group: symmetry
explevel: expert
c3sym_seg3_1
default: ‘’
type: string
title: Segment ID of third C3 segment
short description: Segment ID of third C3 segment
long description: Segment ID of third C3 segment
group: symmetry
explevel: expert
c3sym_sta1_1
default: nan
type: integer
title: Residue number of first residue
min: -9999
max: 9999
short description: Residue number of first residue in the first C3 symmetry segment
long description: Residue number of first residue in the first C3 symmetry segment
group: symmetry
explevel: expert
c3sym_sta2_1
default: nan
type: integer
title: Residue number of first residue
min: -9999
max: 9999
short description: Residue number of first residue in the second C3 symmetry segment
long description: Residue number of first residue in the second C3 symmetry segment
group: symmetry
explevel: expert
c3sym_sta3_1
default: nan
type: integer
title: Residue number of first residue
min: -9999
max: 9999
short description: Residue number of first residue in the third C3 symmetry segment
long description: Residue number of first residue in the third C3 symmetry segment
group: symmetry
explevel: expert
c4sym_end1_1
default: nan
type: integer
title: Residue number of last residue
min: -9999
max: 9999
short description: Residue number of last residue in the first C4 symmetry segment
long description: Residue number of last residue in the first C4 symmetry segment
group: symmetry
explevel: expert
c4sym_end2_1
default: nan
type: integer
title: Residue number of last residue
min: -9999
max: 9999
short description: Residue number of last residue in the second C4 symmetry segment
long description: Residue number of last residue in the second C4 symmetry segment
group: symmetry
explevel: expert
c4sym_end3_1
default: nan
type: integer
title: Residue number of last residue
min: -9999
max: 9999
short description: Residue number of last residue in the third C4 symmetry segment
long description: Residue number of last residue in the third C4 symmetry segment
group: symmetry
explevel: expert
c4sym_end4_1
default: nan
type: integer
title: Residue number of last residue
min: -9999
max: 9999
short description: Residue number of last residue in the fourth C4 symmetry segment
long description: Residue number of last residue in the fourth C4 symmetry segment
group: symmetry
explevel: expert
c4sym_seg1_1
default: ‘’
type: string
title: Segment ID of first C4 segment
short description: Segment ID of first C4 segment
long description: Segment ID of first C4 segment
group: symmetry
explevel: expert
c4sym_seg2_1
default: ‘’
type: string
title: Segment ID of second C4 segment
short description: Segment ID of second C4 segment
long description: Segment ID of second C4 segment
group: symmetry
explevel: expert
c4sym_seg3_1
default: ‘’
type: string
title: Segment ID of third C4 segment
short description: Segment ID of third C4 segment
long description: Segment ID of third C4 segment
group: symmetry
explevel: expert
c4sym_seg4_1
default: ‘’
type: string
title: Segment ID of fourth C4 segment
short description: Segment ID of fourth C4 segment
long description: Segment ID of fourth C4 segment
group: symmetry
explevel: expert
c4sym_sta1_1
default: nan
type: integer
title: Residue number of first residue
min: -9999
max: 9999
short description: Residue number of first residue in the first C4 symmetry segment
long description: Residue number of first residue in the first C4 symmetry segment
group: symmetry
explevel: expert
c4sym_sta2_1
default: nan
type: integer
title: Residue number of first residue
min: -9999
max: 9999
short description: Residue number of first residue in the second C4 symmetry segment
long description: Residue number of first residue in the second C4 symmetry segment
group: symmetry
explevel: expert
c4sym_sta3_1
default: nan
type: integer
title: Residue number of first residue
min: -9999
max: 9999
short description: Residue number of first residue in the third C4 symmetry segment
long description: Residue number of first residue in the third C4 symmetry segment
group: symmetry
explevel: expert
c4sym_sta4_1
default: nan
type: integer
title: Residue number of first residue
min: -9999
max: 9999
short description: Residue number of first residue in the fourth C4 symmetry segment
long description: Residue number of first residue in the fourth C4 symmetry segment
group: symmetry
explevel: expert
c5sym_end1_1
default: nan
type: integer
title: Residue number of last residue
min: -9999
max: 9999
short description: Residue number of last residue in the first C5 symmetry segment
long description: Residue number of last residue in the first C5 symmetry segment
group: symmetry
explevel: expert
c5sym_end2_1
default: nan
type: integer
title: Residue number of last residue
min: -9999
max: 9999
short description: Residue number of last residue in the second C5 symmetry segment
long description: Residue number of last residue in the second C5 symmetry segment
group: symmetry
explevel: expert
c5sym_end3_1
default: nan
type: integer
title: Residue number of last residue
min: -9999
max: 9999
short description: Residue number of last residue in the third C5 symmetry segment
long description: Residue number of last residue in the third C5 symmetry segment
group: symmetry
explevel: expert
c5sym_end4_1
default: nan
type: integer
title: Residue number of last residue
min: -9999
max: 9999
short description: Residue number of last residue in the fourth C5 symmetry segment
long description: Residue number of last residue in the fourth C5 symmetry segment
group: symmetry
explevel: expert
c5sym_end5_1
default: nan
type: integer
title: Residue number of last residue
min: -9999
max: 9999
short description: Residue number of last residue in the fifth C5 symmetry segment
long description: Residue number of last residue in the fifth C5 symmetry segment
group: symmetry
explevel: expert
c5sym_seg1_1
default: ‘’
type: string
title: Segment ID of first C5 segment
short description: Segment ID of first C5 segment
long description: Segment ID of first C5 segment
group: symmetry
explevel: expert
c5sym_seg2_1
default: ‘’
type: string
title: Segment ID of second C5 segment
short description: Segment ID of second C5 segment
long description: Segment ID of second C5 segment
group: symmetry
explevel: expert
c5sym_seg3_1
default: ‘’
type: string
title: Segment ID of third C5 segment
short description: Segment ID of third C5 segment
long description: Segment ID of third C5 segment
group: symmetry
explevel: expert
c5sym_seg4_1
default: ‘’
type: string
title: Segment ID of fourth C5 segment
short description: Segment ID of fourth C5 segment
long description: Segment ID of fourth C5 segment
group: symmetry
explevel: expert
c5sym_seg5_1
default: ‘’
type: string
title: Segment ID of fifth C5 segment
short description: Segment ID of fifth C5 segment
long description: Segment ID of fifth C5 segment
group: symmetry
explevel: expert
c5sym_sta1_1
default: nan
type: integer
title: Residue number of first residue
min: -9999
max: 9999
short description: Residue number of first residue in the first C5 symmetry segment
long description: Residue number of first residue in the first C5 symmetry segment
group: symmetry
explevel: expert
c5sym_sta2_1
default: nan
type: integer
title: Residue number of first residue
min: -9999
max: 9999
short description: Residue number of first residue in the second C5 symmetry segment
long description: Residue number of first residue in the second C5 symmetry segment
group: symmetry
explevel: expert
c5sym_sta3_1
default: nan
type: integer
title: Residue number of first residue
min: -9999
max: 9999
short description: Residue number of first residue in the third C5 symmetry segment
long description: Residue number of first residue in the third C5 symmetry segment
group: symmetry
explevel: expert
c5sym_sta4_1
default: nan
type: integer
title: Residue number of first residue
min: -9999
max: 9999
short description: Residue number of first residue in the fourth C5 symmetry segment
long description: Residue number of first residue in the fourth C5 symmetry segment
group: symmetry
explevel: expert
c5sym_sta5_1
default: nan
type: integer
title: Residue number of first residue
min: -9999
max: 9999
short description: Residue number of first residue in the fifth C5 symmetry segment
long description: Residue number of first residue in the fifth C5 symmetry segment
group: symmetry
explevel: expert
c6sym_end1_1
default: nan
type: integer
title: Residue number of last residue
min: -9999
max: 9999
short description: Residue number of last residue in the first C6 symmetry segment
long description: Residue number of last residue in the first C6 symmetry segment
group: symmetry
explevel: expert
c6sym_end2_1
default: nan
type: integer
title: Residue number of last residue
min: -9999
max: 9999
short description: Residue number of last residue in the second C6 symmetry segment
long description: Residue number of last residue in the second C6 symmetry segment
group: symmetry
explevel: expert
c6sym_end3_1
default: nan
type: integer
title: Residue number of last residue
min: -9999
max: 9999
short description: Residue number of last residue in the third C6 symmetry segment
long description: Residue number of last residue in the third C6 symmetry segment
group: symmetry
explevel: expert
c6sym_end4_1
default: nan
type: integer
title: Residue number of last residue
min: -9999
max: 9999
short description: Residue number of last residue in the fourth C6 symmetry segment
long description: Residue number of last residue in the fourth C6 symmetry segment
group: symmetry
explevel: expert
c6sym_end5_1
default: nan
type: integer
title: Residue number of last residue
min: -9999
max: 9999
short description: Residue number of last residue in the fifth C6 symmetry segment
long description: Residue number of last residue in the fifth C6 symmetry segment
group: symmetry
explevel: expert
c6sym_end6_1
default: nan
type: integer
title: Residue number of last residue
min: -9999
max: 9999
short description: Residue number of last residue in the sixth C6 symmetry segment
long description: Residue number of last residue in the sixth C6 symmetry segment
group: symmetry
explevel: expert
c6sym_seg1_1
default: ‘’
type: string
title: Segment ID of first C6 segment
short description: Segment ID of first C6 segment
long description: Segment ID of first C6 segment
group: symmetry
explevel: expert
c6sym_seg2_1
default: ‘’
type: string
title: Segment ID of second C6 segment
short description: Segment ID of second C6 segment
long description: Segment ID of second C6 segment
group: symmetry
explevel: expert
c6sym_seg3_1
default: ‘’
type: string
title: Segment ID of third C6 segment
short description: Segment ID of third C6 segment
long description: Segment ID of third C6 segment
group: symmetry
explevel: expert
c6sym_seg4_1
default: ‘’
type: string
title: Segment ID of fourth C6 segment
short description: Segment ID of fourth C6 segment
long description: Segment ID of fourth C6 segment
group: symmetry
explevel: expert
c6sym_seg5_1
default: ‘’
type: string
title: Segment ID of fifth C6 segment
short description: Segment ID of fifth C6 segment
long description: Segment ID of fifth C6 segment
group: symmetry
explevel: expert
c6sym_seg6_1
default: ‘’
type: string
title: Segment ID of sixth C6 segment
short description: Segment ID of sixth C6 segment
long description: Segment ID of sixth C6 segment
group: symmetry
explevel: expert
c6sym_sta1_1
default: nan
type: integer
title: Residue number of first residue
min: -9999
max: 9999
short description: Residue number of first residue in the first C6 symmetry segment
long description: Residue number of first residue in the first C6 symmetry segment
group: symmetry
explevel: expert
c6sym_sta2_1
default: nan
type: integer
title: Residue number of first residue
min: -9999
max: 9999
short description: Residue number of first residue in the second C6 symmetry segment
long description: Residue number of first residue in the second C6 symmetry segment
group: symmetry
explevel: expert
c6sym_sta3_1
default: nan
type: integer
title: Residue number of first residue
min: -9999
max: 9999
short description: Residue number of first residue in the third C6 symmetry segment
long description: Residue number of first residue in the third C6 symmetry segment
group: symmetry
explevel: expert
c6sym_sta4_1
default: nan
type: integer
title: Residue number of first residue
min: -9999
max: 9999
short description: Residue number of first residue in the fourth C6 symmetry segment
long description: Residue number of first residue in the fourth C6 symmetry segment
group: symmetry
explevel: expert
c6sym_sta5_1
default: nan
type: integer
title: Residue number of first residue
min: -9999
max: 9999
short description: Residue number of first residue in the fifth C6 symmetry segment
long description: Residue number of first residue in the fifth C6 symmetry segment
group: symmetry
explevel: expert
c6sym_sta6_1
default: nan
type: integer
title: Residue number of first residue
min: -9999
max: 9999
short description: Residue number of first residue in the sixth C6 symmetry segment
long description: Residue number of first residue in the sixth C6 symmetry segment
group: symmetry
explevel: expert
cmrest
default: False
type: boolean
title: Center of mass restraints
short description: Automatically defines distance restraints between the geometric center of the various molecules.
long description: When turned on, this option will automatically define center of mass restraints between the various molecules. This allows HADDOCK to operate in ab-initio mode in the absence of any other restraints. But those restraints can also be combined with other restraints to ensure more compact solutions. The distance restraints are defined between the geometrical centers of the various molecules (calculated on CA atoms for proteins (BB in case of Martini coarse-grained molecules) and N1 atoms for nucleic acids. For small ligands, all atoms will be used to define the geometric center. The upper limit distance is automatically calculated based on the dimension of the molecules (see cmtight description).
group: ab initio mode
explevel: expert
cmtight
default: True
type: boolean
title: Center of mass restraint tightness
short description: Defines the upper distance limit based on the sum of the average dimension of the two molecule, if cmtight=false all three dimensions are used, if set to true the shortest two only are used, resulting in tighter distance restraints.
long description: This parameter controls how the upper limit distance is defined for the center of mass restraints between molecules. Each molecule is oriented along its principle components and the x,y and z dimensions are calculated. If cmtight=true, the molecule distance (size) is set to the average of its smallest two half dimensions. If cmtight=false, the molecule distance (size) is set to the average of its three half dimensions.. In case of DNA or small ligands the molecule distance (size) is set to 0. The effective upper distance limit for the center or mass distance restraint is the sum of the two molecule distances.
group: ab initio mode
explevel: expert
crossdock
default: True
type: boolean
title: Cross docking of starting ensembles
short description: In case ensembles of starting structures are provided, if set to true, takes all possible combinations for the docking.
long description: This variable controls on starting models are combined in case ensembles of starting structures are provided. If set to true, all possible combinations of starting models will be used for the docking. If set to false, the first model from molecule1 will be combined with the first model from molecule2 and so on.
group: sampling
explevel: expert
dielec
default: ‘rdie’
type: string
title: Constant (cdie) or distance-dependent dielectric (rdie) constant.
choices: [‘cdie’, ‘rdie’]
short description: Use a constant (cdie option) or a distance-dependent dielectric (rdie) constant in the Coulomb potential.
long description: Use a constant (cdie option) or a distance-dependent dielectric (rdie) constant in the Coulomb potential. A distance dependent dielectric constant will effectively scale down the electrostatic energy by having a 1/r**2 dependency instead of 1/r
group: force field
explevel: expert
epsilon
default: 10.0
type: float
title: Dielectric constant
min: 1
max: 78
short description: Dielectric constant for the electrostatic Coulomb energy term.
long description: Dielectric constant for the electrostatic Coulomb energy term.
group: force field
explevel: expert
hbond_scale
default: 50
type: integer
title: Force constant for hbonds distance restraints
min: 0
max: 1000
short description: Force constant applied to the distance restraints defined in hbond_fname.
long description: Force constant applied to the distance restraints defined in hbond_fname.
group: distance restraints
explevel: expert
inter_rigid
default: 1.0
type: float
title: Scaling of intermolecular interactions
min: 0
max: 1
short description: Scaling of intermolecular interactions
long description: Scaling of intermolecular interactions. This allows in particular to scale down intermolecular interactions to reach buried sites (recommended value for this is 0.01). If scaled-down do note that the van der Waals intermolecular energy might be bad because of clashes. In that case it is best to also set the weight of the van der Waals energy term to 0 (w_vdw).
group: sampling
explevel: expert
kcm
default: 1.0
type: float
title: Center of mass restraints force constant
min: 0
max: 1000
short description: Force constant applied to the center of mass restraints
long description: Force constant applied to the center of mass restraints
group: ab initio mode
explevel: expert
ksurf
default: 1.0
type: float
title: Surface contact restraints force constant
min: 0
max: 1000
short description: Force constant applied to the surface contact restraints.
long description: Force constant applied to the surface contact restraints.
group: ab initio mode
explevel: expert
ksym
default: 10.0
type: float
title: Force constant for symmetry restraints
min: 0
max: 1000
short description: Force constant for symmetry restraints
long description: Force constant for symmetry restraints
group: symmetry
explevel: expert
ligand_param_fname
default: ‘’
type: file
title: Custom ligand parameter file
short description: Ligand parameter file in CNS format
long description: Ligand parameter file in CNS format containing all force field parameters (bond, angles, dihedrals, impropers, van der waals) for any ligand not supported by default by HADDOCK
group: force field
explevel: expert
ligand_top_fname
default: ‘’
type: file
title: Custom ligand topology file
short description: Ligand topology file in CNS format
long description: Ligand topology file in CNS format containing the ligand topologies (atoms, masses, charges, bond definitions…) for any ligand not supported by default by HADDOCK
group: force field
explevel: expert
mol_fix_origin_1
default: False
type: boolean
title: Fix molecule
short description: Fixes the molecule in its original position.
long description: Fixes the molecule in its original position.
group: molecule
explevel: expert
nc2sym
default: 0
type: integer
title: Number of C2 symmetry restraints
min: 0
max: 40
short description: Defines the number of C2 symmetry restraints.
long description: Defines the number of C2 symmetry restraints. For each, a pair of segments on which the symmetry restraint is applied will have to be defined. Those must all have the same length.
group: symmetry
explevel: expert
nc3sym
default: 0
type: integer
title: Number of C3 symmetry restraints
min: 0
max: 10
short description: Defines the number of C3 symmetry restraints.
long description: Defines the number of C3 symmetry restraints. For each, three segments on which the symmetry restraint is applied will have to be defined. Those must all have the same length.
group: symmetry
explevel: expert
nc4sym
default: 0
type: integer
title: Number of C4 symmetry restraints
min: 0
max: 10
short description: Defines the number of C4 symmetry restraints.
long description: Defines the number of C4 symmetry restraints. For each, four segments on which the symmetry restraint is applied will have to be defined. Those must all have the same length.
group: symmetry
explevel: expert
nc5sym
default: 0
type: integer
title: Number of C5 symmetry restraints
min: 0
max: 10
short description: Defines the number of C5 symmetry restraints.
long description: Defines the number of C5 symmetry restraints. For each, five segments on which the symmetry restraint is applied will have to be defined. Those must all have the same length.
group: symmetry
explevel: expert
nc6sym
default: 0
type: integer
title: Number of C6 symmetry restraints
min: 0
max: 10
short description: Defines the number of C6 symmetry restraints.
long description: Defines the number of C6 symmetry restraints. For each, six segments on which the symmetry restraint is applied will have to be defined. Those must all have the same length.
group: symmetry
explevel: expert
npart
default: 2
type: integer
title: Number partitions for ambiguous restraints
min: 1
max: 20
short description: Number of sets into which to randomly partition the ambiguous restraints.
long description: Number of sets into which to randomly partition the ambiguous restraints. The fraction of restraints randomly removed depends on the npart parameter which defines in how many sets the restraints should be randomly split. The first set will be removed. The fraction of randomly removed ambiguous restraints is thus 1/npart.
group: distance restraints
explevel: expert
nrair_1
default: 0
type: integer
title: Number of segments from which to pick random restraints
min: 0
max: 100
short description: Defines the number of segments for this molecule from which to randomly define random interaction restraints.
long description: Defines the number of segments for this molecule from which to randomly define random interaction restraints. Only solvent accessible residues will be considered. See also the ranair parameter.
group: ab initio mode
explevel: expert
nrair_10
default: 0
type: integer
title: Number of segments from which to pick random restraints
min: 0
max: 100
short description: Defines the number of segments for this molecule from which to randomly define random interaction restraints.
long description: Defines the number of segments for this molecule from which to randomly define random interaction restraints. Only solvent accessible residues will be considered. See also the ranair parameter.
group: ab initio mode
explevel: expert
nrair_11
default: 0
type: integer
title: Number of segments from which to pick random restraints
min: 0
max: 100
short description: Defines the number of segments for this molecule from which to randomly define random interaction restraints.
long description: Defines the number of segments for this molecule from which to randomly define random interaction restraints. Only solvent accessible residues will be considered. See also the ranair parameter.
group: ab initio mode
explevel: expert
nrair_12
default: 0
type: integer
title: Number of segments from which to pick random restraints
min: 0
max: 100
short description: Defines the number of segments for this molecule from which to randomly define random interaction restraints.
long description: Defines the number of segments for this molecule from which to randomly define random interaction restraints. Only solvent accessible residues will be considered. See also the ranair parameter.
group: ab initio mode
explevel: expert
nrair_13
default: 0
type: integer
title: Number of segments from which to pick random restraints
min: 0
max: 100
short description: Defines the number of segments for this molecule from which to randomly define random interaction restraints.
long description: Defines the number of segments for this molecule from which to randomly define random interaction restraints. Only solvent accessible residues will be considered. See also the ranair parameter.
group: ab initio mode
explevel: expert
nrair_14
default: 0
type: integer
title: Number of segments from which to pick random restraints
min: 0
max: 100
short description: Defines the number of segments for this molecule from which to randomly define random interaction restraints.
long description: Defines the number of segments for this molecule from which to randomly define random interaction restraints. Only solvent accessible residues will be considered. See also the ranair parameter.
group: ab initio mode
explevel: expert
nrair_15
default: 0
type: integer
title: Number of segments from which to pick random restraints
min: 0
max: 100
short description: Defines the number of segments for this molecule from which to randomly define random interaction restraints.
long description: Defines the number of segments for this molecule from which to randomly define random interaction restraints. Only solvent accessible residues will be considered. See also the ranair parameter.
group: ab initio mode
explevel: expert
nrair_16
default: 0
type: integer
title: Number of segments from which to pick random restraints
min: 0
max: 100
short description: Defines the number of segments for this molecule from which to randomly define random interaction restraints.
long description: Defines the number of segments for this molecule from which to randomly define random interaction restraints. Only solvent accessible residues will be considered. See also the ranair parameter.
group: ab initio mode
explevel: expert
nrair_17
default: 0
type: integer
title: Number of segments from which to pick random restraints
min: 0
max: 100
short description: Defines the number of segments for this molecule from which to randomly define random interaction restraints.
long description: Defines the number of segments for this molecule from which to randomly define random interaction restraints. Only solvent accessible residues will be considered. See also the ranair parameter.
group: ab initio mode
explevel: expert
nrair_18
default: 0
type: integer
title: Number of segments from which to pick random restraints
min: 0
max: 100
short description: Defines the number of segments for this molecule from which to randomly define random interaction restraints.
long description: Defines the number of segments for this molecule from which to randomly define random interaction restraints. Only solvent accessible residues will be considered. See also the ranair parameter.
group: ab initio mode
explevel: expert
nrair_19
default: 0
type: integer
title: Number of segments from which to pick random restraints
min: 0
max: 100
short description: Defines the number of segments for this molecule from which to randomly define random interaction restraints.
long description: Defines the number of segments for this molecule from which to randomly define random interaction restraints. Only solvent accessible residues will be considered. See also the ranair parameter.
group: ab initio mode
explevel: expert
nrair_2
default: 0
type: integer
title: Number of segments from which to pick random restraints
min: 0
max: 100
short description: Defines the number of segments for this molecule from which to randomly define random interaction restraints.
long description: Defines the number of segments for this molecule from which to randomly define random interaction restraints. Only solvent accessible residues will be considered. See also the ranair parameter.
group: ab initio mode
explevel: expert
nrair_20
default: 0
type: integer
title: Number of segments from which to pick random restraints
min: 0
max: 100
short description: Defines the number of segments for this molecule from which to randomly define random interaction restraints.
long description: Defines the number of segments for this molecule from which to randomly define random interaction restraints. Only solvent accessible residues will be considered. See also the ranair parameter.
group: ab initio mode
explevel: expert
nrair_3
default: 0
type: integer
title: Number of segments from which to pick random restraints
min: 0
max: 100
short description: Defines the number of segments for this molecule from which to randomly define random interaction restraints.
long description: Defines the number of segments for this molecule from which to randomly define random interaction restraints. Only solvent accessible residues will be considered. See also the ranair parameter.
group: ab initio mode
explevel: expert
nrair_4
default: 0
type: integer
title: Number of segments from which to pick random restraints
min: 0
max: 100
short description: Defines the number of segments for this molecule from which to randomly define random interaction restraints.
long description: Defines the number of segments for this molecule from which to randomly define random interaction restraints. Only solvent accessible residues will be considered. See also the ranair parameter.
group: ab initio mode
explevel: expert
nrair_5
default: 0
type: integer
title: Number of segments from which to pick random restraints
min: 0
max: 100
short description: Defines the number of segments for this molecule from which to randomly define random interaction restraints.
long description: Defines the number of segments for this molecule from which to randomly define random interaction restraints. Only solvent accessible residues will be considered. See also the ranair parameter.
group: ab initio mode
explevel: expert
nrair_6
default: 0
type: integer
title: Number of segments from which to pick random restraints
min: 0
max: 100
short description: Defines the number of segments for this molecule from which to randomly define random interaction restraints.
long description: Defines the number of segments for this molecule from which to randomly define random interaction restraints. Only solvent accessible residues will be considered. See also the ranair parameter.
group: ab initio mode
explevel: expert
nrair_7
default: 0
type: integer
title: Number of segments from which to pick random restraints
min: 0
max: 100
short description: Defines the number of segments for this molecule from which to randomly define random interaction restraints.
long description: Defines the number of segments for this molecule from which to randomly define random interaction restraints. Only solvent accessible residues will be considered. See also the ranair parameter.
group: ab initio mode
explevel: expert
nrair_8
default: 0
type: integer
title: Number of segments from which to pick random restraints
min: 0
max: 100
short description: Defines the number of segments for this molecule from which to randomly define random interaction restraints.
long description: Defines the number of segments for this molecule from which to randomly define random interaction restraints. Only solvent accessible residues will be considered. See also the ranair parameter.
group: ab initio mode
explevel: expert
nrair_9
default: 0
type: integer
title: Number of segments from which to pick random restraints
min: 0
max: 100
short description: Defines the number of segments for this molecule from which to randomly define random interaction restraints.
long description: Defines the number of segments for this molecule from which to randomly define random interaction restraints. Only solvent accessible residues will be considered. See also the ranair parameter.
group: ab initio mode
explevel: expert
ns3sym
default: 0
type: integer
title: Number of S3 symmetry restraints
min: 0
max: 10
short description: Defines the number of S3 symmetry restraints.
long description: Defines the number of S3 symmetry restraints. For each, three segments on which the symmetry restraint is applied will have to be defined. Those must all have the same length.
group: symmetry
explevel: expert
ntrials
default: 5
type: integer
title: Number of internal docking trials
min: 1
max: 100
short description: Number of internal docking trials. Only the best model will be written to disk.
long description: Number of internal docking trials. HADDOCK will repeat the docking internally multiple times, ranking them internally and only writing the best model to disk.
group: sampling
explevel: expert
previous_ambig
default: False
type: boolean
title: Boolean condition on the previous ambiguous distance restraints file
short description: Boolean condition on the previous ambiguous distance restraints file. If true, use the the restraint information coming from the previous CNS module. If false, don’t use previous information.
long description: Boolean condition on the ambiguous distance restraints file. If true, use the restraint information coming from the previous CNS module, as long as an ambig_fname is not defined for the current module. If false, don’t use previous information.
group: distance restraints
explevel: expert
rair_end_10_1
default: nan
type: integer
title: Ending residue number
min: -9999
max: 9999
short description: Ending residue number for segment from which to define random interaction restraints
long description: Ending residue number for segment from which to define random interaction restraints
group: ab initio mode
explevel: expert
rair_end_11_1
default: nan
type: integer
title: Ending residue number
min: -9999
max: 9999
short description: Ending residue number for segment from which to define random interaction restraints
long description: Ending residue number for segment from which to define random interaction restraints
group: ab initio mode
explevel: expert
rair_end_12_1
default: nan
type: integer
title: Ending residue number
min: -9999
max: 9999
short description: Ending residue number for segment from which to define random interaction restraints
long description: Ending residue number for segment from which to define random interaction restraints
group: ab initio mode
explevel: expert
rair_end_13_1
default: nan
type: integer
title: Ending residue number
min: -9999
max: 9999
short description: Ending residue number for segment from which to define random interaction restraints
long description: Ending residue number for segment from which to define random interaction restraints
group: ab initio mode
explevel: expert
rair_end_14_1
default: nan
type: integer
title: Ending residue number
min: -9999
max: 9999
short description: Ending residue number for segment from which to define random interaction restraints
long description: Ending residue number for segment from which to define random interaction restraints
group: ab initio mode
explevel: expert
rair_end_15_1
default: nan
type: integer
title: Ending residue number
min: -9999
max: 9999
short description: Ending residue number for segment from which to define random interaction restraints
long description: Ending residue number for segment from which to define random interaction restraints
group: ab initio mode
explevel: expert
rair_end_16_1
default: nan
type: integer
title: Ending residue number
min: -9999
max: 9999
short description: Ending residue number for segment from which to define random interaction restraints
long description: Ending residue number for segment from which to define random interaction restraints
group: ab initio mode
explevel: expert
rair_end_17_1
default: nan
type: integer
title: Ending residue number
min: -9999
max: 9999
short description: Ending residue number for segment from which to define random interaction restraints
long description: Ending residue number for segment from which to define random interaction restraints
group: ab initio mode
explevel: expert
rair_end_18_1
default: nan
type: integer
title: Ending residue number
min: -9999
max: 9999
short description: Ending residue number for segment from which to define random interaction restraints
long description: Ending residue number for segment from which to define random interaction restraints
group: ab initio mode
explevel: expert
rair_end_19_1
default: nan
type: integer
title: Ending residue number
min: -9999
max: 9999
short description: Ending residue number for segment from which to define random interaction restraints
long description: Ending residue number for segment from which to define random interaction restraints
group: ab initio mode
explevel: expert
rair_end_1_1
default: nan
type: integer
title: Ending residue number
min: -9999
max: 9999
short description: Ending residue number for segment from which to define random interaction restraints
long description: Ending residue number for segment from which to define random interaction restraints
group: ab initio mode
explevel: expert
rair_end_20_1
default: nan
type: integer
title: Ending residue number
min: -9999
max: 9999
short description: Ending residue number for segment from which to define random interaction restraints
long description: Ending residue number for segment from which to define random interaction restraints
group: ab initio mode
explevel: expert
rair_end_2_1
default: nan
type: integer
title: Ending residue number
min: -9999
max: 9999
short description: Ending residue number for segment from which to define random interaction restraints
long description: Ending residue number for segment from which to define random interaction restraints
group: ab initio mode
explevel: expert
rair_end_3_1
default: nan
type: integer
title: Ending residue number
min: -9999
max: 9999
short description: Ending residue number for segment from which to define random interaction restraints
long description: Ending residue number for segment from which to define random interaction restraints
group: ab initio mode
explevel: expert
rair_end_4_1
default: nan
type: integer
title: Ending residue number
min: -9999
max: 9999
short description: Ending residue number for segment from which to define random interaction restraints
long description: Ending residue number for segment from which to define random interaction restraints
group: ab initio mode
explevel: expert
rair_end_5_1
default: nan
type: integer
title: Ending residue number
min: -9999
max: 9999
short description: Ending residue number for segment from which to define random interaction restraints
long description: Ending residue number for segment from which to define random interaction restraints
group: ab initio mode
explevel: expert
rair_end_6_1
default: nan
type: integer
title: Ending residue number
min: -9999
max: 9999
short description: Ending residue number for segment from which to define random interaction restraints
long description: Ending residue number for segment from which to define random interaction restraints
group: ab initio mode
explevel: expert
rair_end_7_1
default: nan
type: integer
title: Ending residue number
min: -9999
max: 9999
short description: Ending residue number for segment from which to define random interaction restraints
long description: Ending residue number for segment from which to define random interaction restraints
group: ab initio mode
explevel: expert
rair_end_8_1
default: nan
type: integer
title: Ending residue number
min: -9999
max: 9999
short description: Ending residue number for segment from which to define random interaction restraints
long description: Ending residue number for segment from which to define random interaction restraints
group: ab initio mode
explevel: expert
rair_end_9_1
default: nan
type: integer
title: Ending residue number
min: -9999
max: 9999
short description: Ending residue number for segment from which to define random interaction restraints
long description: Ending residue number for segment from which to define random interaction restraints
group: ab initio mode
explevel: expert
rair_sta_10_1
default: nan
type: integer
title: Starting residue number
min: -9999
max: 9999
short description: Starting residue number for segment from which to define random interaction restraints
long description: Starting residue number for segment from which to define random interaction restraints
group: ab initio mode
explevel: expert
rair_sta_11_1
default: nan
type: integer
title: Starting residue number
min: -9999
max: 9999
short description: Starting residue number for segment from which to define random interaction restraints
long description: Starting residue number for segment from which to define random interaction restraints
group: ab initio mode
explevel: expert
rair_sta_12_1
default: nan
type: integer
title: Starting residue number
min: -9999
max: 9999
short description: Starting residue number for segment from which to define random interaction restraints
long description: Starting residue number for segment from which to define random interaction restraints
group: ab initio mode
explevel: expert
rair_sta_13_1
default: nan
type: integer
title: Starting residue number
min: -9999
max: 9999
short description: Starting residue number for segment from which to define random interaction restraints
long description: Starting residue number for segment from which to define random interaction restraints
group: ab initio mode
explevel: expert
rair_sta_14_1
default: nan
type: integer
title: Starting residue number
min: -9999
max: 9999
short description: Starting residue number for segment from which to define random interaction restraints
long description: Starting residue number for segment from which to define random interaction restraints
group: ab initio mode
explevel: expert
rair_sta_15_1
default: nan
type: integer
title: Starting residue number
min: -9999
max: 9999
short description: Starting residue number for segment from which to define random interaction restraints
long description: Starting residue number for segment from which to define random interaction restraints
group: ab initio mode
explevel: expert
rair_sta_16_1
default: nan
type: integer
title: Starting residue number
min: -9999
max: 9999
short description: Starting residue number for segment from which to define random interaction restraints
long description: Starting residue number for segment from which to define random interaction restraints
group: ab initio mode
explevel: expert
rair_sta_17_1
default: nan
type: integer
title: Starting residue number
min: -9999
max: 9999
short description: Starting residue number for segment from which to define random interaction restraints
long description: Starting residue number for segment from which to define random interaction restraints
group: ab initio mode
explevel: expert
rair_sta_18_1
default: nan
type: integer
title: Starting residue number
min: -9999
max: 9999
short description: Starting residue number for segment from which to define random interaction restraints
long description: Starting residue number for segment from which to define random interaction restraints
group: ab initio mode
explevel: expert
rair_sta_19_1
default: nan
type: integer
title: Starting residue number
min: -9999
max: 9999
short description: Starting residue number for segment from which to define random interaction restraints
long description: Starting residue number for segment from which to define random interaction restraints
group: ab initio mode
explevel: expert
rair_sta_1_1
default: nan
type: integer
title: Starting residue number
min: -9999
max: 9999
short description: Starting residue number for segment from which to define random interaction restraints
long description: Starting residue number for segment from which to define random interaction restraints
group: ab initio mode
explevel: expert
rair_sta_20_1
default: nan
type: integer
title: Starting residue number
min: -9999
max: 9999
short description: Starting residue number for segment from which to define random interaction restraints
long description: Starting residue number for segment from which to define random interaction restraints
group: ab initio mode
explevel: expert
rair_sta_2_1
default: nan
type: integer
title: Starting residue number
min: -9999
max: 9999
short description: Starting residue number for segment from which to define random interaction restraints
long description: Starting residue number for segment from which to define random interaction restraints
group: ab initio mode
explevel: expert
rair_sta_3_1
default: nan
type: integer
title: Starting residue number
min: -9999
max: 9999
short description: Starting residue number for segment from which to define random interaction restraints
long description: Starting residue number for segment from which to define random interaction restraints
group: ab initio mode
explevel: expert
rair_sta_4_1
default: nan
type: integer
title: Starting residue number
min: -9999
max: 9999
short description: Starting residue number for segment from which to define random interaction restraints
long description: Starting residue number for segment from which to define random interaction restraints
group: ab initio mode
explevel: expert
rair_sta_5_1
default: nan
type: integer
title: Starting residue number
min: -9999
max: 9999
short description: Starting residue number for segment from which to define random interaction restraints
long description: Starting residue number for segment from which to define random interaction restraints
group: ab initio mode
explevel: expert
rair_sta_6_1
default: nan
type: integer
title: Starting residue number
min: -9999
max: 9999
short description: Starting residue number for segment from which to define random interaction restraints
long description: Starting residue number for segment from which to define random interaction restraints
group: ab initio mode
explevel: expert
rair_sta_7_1
default: nan
type: integer
title: Starting residue number
min: -9999
max: 9999
short description: Starting residue number for segment from which to define random interaction restraints
long description: Starting residue number for segment from which to define random interaction restraints
group: ab initio mode
explevel: expert
rair_sta_8_1
default: nan
type: integer
title: Starting residue number
min: -9999
max: 9999
short description: Starting residue number for segment from which to define random interaction restraints
long description: Starting residue number for segment from which to define random interaction restraints
group: ab initio mode
explevel: expert
rair_sta_9_1
default: nan
type: integer
title: Starting residue number
min: -9999
max: 9999
short description: Starting residue number for segment from which to define random interaction restraints
long description: Starting residue number for segment from which to define random interaction restraints
group: ab initio mode
explevel: expert
ranair
default: False
type: boolean
title: Random interaction restraints
short description: Ambiguous interaction restraints will be defined randomly from surface patches around solvent accessible residues.
long description: When turned on, this option will automatically define ambigous interaction restraints between the various molecules from randomly selected surface patches from solvent accessible residues . This allows HADDOCK to operate in ab-initio mode. Note that this type of restraints can not be combined with any other distance restraints. By default the entire surface will be sampled, but it is possible to define per molecule segments from which the random restraints will be defined (see the nrair_X parameter).
group: ab initio mode
explevel: expert
randremoval
default: True
type: boolean
title: Random removal of ambiguous restraints
short description: If set to true (default) this will cause the random removal of ambiguous restraints for each model generated.
long description: If set to true (default) this will cause the random removal of ambiguous restraints for each model generated. The fraction of restraints randomly removed depends on the npart parameter which defines in how many sets the restraints should be randomly split. The first set will be removed. The fraction of randomly removed ambiguous restraints is thus 1/npart.
group: distance restraints
explevel: expert
rotate180
default: True
type: boolean
title: Sample 180-rotated solutions
short description: If true, HADDOCK will rotate the molecule by 180 degree around an axis perpendicular to the interface.
long description: This parameter controls the sampling of 180 degree rotated solutions. If set to true, HADDOCK will rotate the molecule by 180 degree around an axis perpendicular to the interface.
group: sampling
explevel: expert
s3sym_end1_1
default: nan
type: integer
title: Residue number of last residue
min: -9999
max: 9999
short description: Residue number of last residue in the first S3 symmetry segment
long description: Residue number of last residue in the first S3 symmetry segment
group: symmetry
explevel: expert
s3sym_end2_1
default: nan
type: integer
title: Residue number of last residue
min: -9999
max: 9999
short description: Residue number of last residue in the second S3 symmetry segment
long description: Residue number of last residue in the second S3 symmetry segment
group: symmetry
explevel: expert
s3sym_end3_1
default: nan
type: integer
title: Residue number of last residue
min: -9999
max: 9999
short description: Residue number of last residue in the third S3 symmetry segment
long description: Residue number of last residue in the third S3 symmetry segment
group: symmetry
explevel: expert
s3sym_seg1_1
default: ‘’
type: string
title: Segment ID of first S3 segment
short description: Segment ID of first S3 segment
long description: Segment ID of first S3 segment
group: symmetry
explevel: expert
s3sym_seg2_1
default: ‘’
type: string
title: Segment ID of second S3 segment
short description: Segment ID of second S3 segment
long description: Segment ID of second S3 segment
group: symmetry
explevel: expert
s3sym_seg3_1
default: ‘’
type: string
title: Segment ID of third S3 segment
short description: Segment ID of third S3 segment
long description: Segment ID of third S3 segment
group: symmetry
explevel: expert
s3sym_sta1_1
default: nan
type: integer
title: Residue number of first residue
min: -9999
max: 9999
short description: Residue number of first residue in the first S3 symmetry segment
long description: Residue number of first residue in the first S3 symmetry segment
group: symmetry
explevel: expert
s3sym_sta2_1
default: nan
type: integer
title: Residue number of first residue
min: -9999
max: 9999
short description: Residue number of first residue in the second S3 symmetry segment
long description: Residue number of first residue in the second S3 symmetry segment
group: symmetry
explevel: expert
s3sym_sta3_1
default: nan
type: integer
title: Residue number of first residue
min: -9999
max: 9999
short description: Residue number of first residue in the third S3 symmetry segment
long description: Residue number of first residue in the third S3 symmetry segment
group: symmetry
explevel: expert
surfrest
default: False
type: boolean
title: Surface contact restraints
short description: Surface contact restraints between molecules
long description: Surface contact restraints between molecules. These are defined as an ambiguous distance restraint between all CA,BB or N1 atoms of two molecules (for small ligands all atoms are considered). The upper limit is set to 7A (or 4.5A in case of small ligands). Note that this option is computationally more expensive than the center of mass restraints (see cmrest).
group: ab initio mode
explevel: expert
sym_on
default: False
type: boolean
title: Symmetry restraints
short description: Enables symmetry restraints
long description: Enables symmetry restraints. The symmetry type (C2,C3,C4,C5,C6,S3 supported) and the segments to which those apply must be defined. In addition a custom symmetry restraint file can be supplied (symrest_fname).
group: symmetry
explevel: expert
symtbl_fname
default: ‘’
type: file
title: Custom symmetry restraints filename
short description: Filename of the custom symmetry restraints file
long description: Filename of the custom symmetry restraints file.
group: symmetry
explevel: expert
tolerance
default: 5
type: integer
title: Failure tolerance percentage
min: 0
max: 99
short description: Percentage of allowed failures for a module to successfully complete
long description: Percentage of allowed failures for a module to successfully complete
group: module
explevel: expert
unambig_scale
default: 50
type: integer
title: Force constant for unambiguous distance restraints
min: 0
max: 1000
short description: Force constant applied to the distance restraints defined in unambig_fname.
long description: Force constant applied to the distance restraints defined in unambig_fname.
group: distance restraints
explevel: expert
w_air
default: 0.01
type: float
title: Weight of the distance restraint energy
min: 0
max: 9999
short description: Weight of the distance restraints energy in the scoring function
long description: Weight of the distance restraints energy in the scoring function. Note that this is different from the force constants used during the calculations.
group: scoring
explevel: expert
w_bsa
default: -0.01
type: float
title: Weight of the buried surface area term
min: -9999
max: 9999
short description: Weight of the buried surface area term in the scoring function
long description: Weight of the buried surface area (BSA) term in the scoring function. Note that the BSA is only used for scoring.
group: scoring
explevel: expert
w_cdih
default: 0.0
type: float
title: Weight of the dihedral angle restraint energy
min: 0
max: 9999
short description: Weight of the dihedral angle restraints energy in the scoring function
long description: Weight of the dihedral angle restraints energy in the scoring function. Note that this is different from the force constant used during the calculations.
group: scoring
explevel: expert
w_desolv
default: 1.0
type: float
title: Weight of the desolvation energy term
min: -9999
max: 9999
short description: Weight of the desolvation energy term in the scoring function
long description: Weight of the desolvation energy term in the scoring function. Note that the desolvation energy is only used for scoring.
group: scoring
explevel: expert
w_dist
default: 0.01
type: float
title: Weight of the distance restraint energy
min: 0
max: 9999
short description: Weight of the distance restraints energy in the scoring function
long description: Weight of the distance restraints energy in the scoring function. Note that this is different from the force constants used during the calculations.
group: scoring
explevel: expert
w_elec
default: 1.0
type: float
title: Weight of the intermolecular electrostatic energy
min: -9999
max: 9999
short description: Weight of the intermolecular electrostatic energy in the scoring function
long description: Weight of the intermolecular electrostatic energy in the scoring function. Note that this does not affect the electostatic energy during the rigidbody minimization.
group: scoring
explevel: expert
w_sym
default: 0.1
type: float
title: Weight of the symmetry restraint energy
min: 0
max: 9999
short description: Weight of the symmetry restraints energy in the scoring function
long description: Weight of the symmetry restraints energy in the scoring function. Note that this is different from the force constant used during the calculations.
group: scoring
explevel: expert
w_vdw
default: 0.01
type: float
title: Weight of the intermolecular van der Waals energy
min: -9999
max: 9999
short description: Weight of the intermolecular van der Waals energy in the scoring function
long description: Weight of the intermolecular van der Waals energy in the scoring function. Note that this does not affect the van der Waals energy during the rigidbody minimization.
group: scoring
explevel: expert
Guru
iniseed
default: 917
type: integer
title: Random seed
min: 0
max: 9999999999999999
short description: Random seed used in CNS to initialize the random seed function
long description: Random seed used in CNS to initialize the random seed function
group: sampling
explevel: guru
keepwater
default: False
type: boolean
title: Write water molecules to output file
short description: Write water molecules if present to the output file.
long description: Write water molecules if present to the output file.
group: sampling
explevel: guru
log_level
default: ‘quiet’
type: string
title: Log level verbosity for CNS
choices: [‘verbose’, ‘normal’, ‘quiet’]
short description: Set the log level verbosity for CNS
long description: CNS, the computational engine used by HADDOCK can generate a lot of output messages. This parameter controls the verbosity of CNS (verbose, normal or quiet).
group: module
explevel: guru
rigidtrans
default: True
type: boolean
title: Allow translation during EM
short description: Enables translation during rigidbody energy minimization
long description: Enables translation during rigidbody energy minimization. If set to false, only a rotational energy minimization will be performed.
group: sampling
explevel: guru