haddock.modules.refinement.cgtoaa package
Module contents
Backmapping of Coarse-Grained structures into All-atom structures with CNS.
The [cgtoaa] module translate the CG conformations into AA representations,
implemented in CNS.
For this module to be functional, it needs to be run in a workflow where [topocg]
is present upstream.
For more details about this module, please refer to the haddock3 user manual
- class haddock.modules.refinement.cgtoaa.HaddockModule(order: int, path: Path, initial_params: str | Path = PosixPath('/opt/hostedtoolcache/Python/3.10.20/x64/lib/python3.10/site-packages/haddock/modules/refinement/cgtoaa/defaults.yaml'))[source]
Bases:
BaseCNSModuleHADDOCK3 module energy minimization refinement.
Default Parameters
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
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: easy
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: 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
Expert
dielec
default: ‘cdie’
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
dihedflag
default: True
type: boolean
title: Use torsion angle dihedral energy term
short description: Turns on the torsion angle dihedral energy terms of the force field.
long description: Turns on the torsion angle dihedral energy terms of the force field.
group: force field
explevel: expert
epsilon
default: 1.0
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
epsilon_cg
default: 10.0
type: float
title: Dielectric constant for coarse-grained mode
min: 1
max: 78
short description: Dielectric constant for the electrostatic Coulomb energy term in coarse-grained mode.
long description: Dielectric constant for the electrostatic Coulomb energy term in coarse-grained mode.
group: force field
explevel: expert
fle_end_1
default: nan
type: integer
title: End residue number
min: -9999
max: 9999
short description: Residue number defining the end of the fully flexible segment.
long description: Residue number defining the end of this (1st) fully flexible segment.
group: flexibility
explevel: expert
fle_seg_1
default: ‘none’
type: string
title: Segment ID (segid)
short description: Segment ID of the molecule for which this flexible segment is defined.
long description: Segment ID of the molecule for which this (1st) flexible segment is defined.
group: flexibility
explevel: expert
fle_sta_1
default: nan
type: integer
title: Starting residue number
min: -9999
max: 9999
short description: Residue number defining the start of the fully flexible segment.
long description: Residue number defining the start of this (1st) fully flexible segment.
group: flexibility
explevel: expert
max_nmodels
default: 50000
type: integer
title: Maximum number of models to refine
min: 1
max: 100000
short description: This parameter controls the maximum number of models to refine.
long description: This parameter controls the maximum number of models to refine.
group: sampling
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
nemsteps
default: 10
type: integer
title: Number of EM steps
min: 1
max: 10000
short description: Number of energy minimisation steps to perform.
long description: Number of energy minimisation steps to perform. Note that the effective number might be smaller if the minimisation converges earlier.
group: sampling
explevel: expert
nseg1
default: -1
type: integer
title: Number of semi-flexible segments
min: -1
max: 1000
short description: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition).
long description: This parameter defines the number of semi-flexible segments for the specified molecule. If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig.
group: flexibility
explevel: expert
nseg10
default: -1
type: integer
title: Number of semi-flexible segments
min: -1
max: 1000
short description: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition).
long description: This parameter defines the number of semi-flexible segments for the specified molecule. If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig.
group: flexibility
explevel: expert
nseg11
default: -1
type: integer
title: Number of semi-flexible segments
min: -1
max: 1000
short description: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition).
long description: This parameter defines the number of semi-flexible segments for the specified molecule. If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig.
group: flexibility
explevel: expert
nseg12
default: -1
type: integer
title: Number of semi-flexible segments
min: -1
max: 1000
short description: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition).
long description: This parameter defines the number of semi-flexible segments for the specified molecule. If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig.
group: flexibility
explevel: expert
nseg13
default: -1
type: integer
title: Number of semi-flexible segments
min: -1
max: 1000
short description: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition).
long description: This parameter defines the number of semi-flexible segments for the specified molecule. If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig.
group: flexibility
explevel: expert
nseg14
default: -1
type: integer
title: Number of semi-flexible segments
min: -1
max: 1000
short description: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition).
long description: This parameter defines the number of semi-flexible segments for the specified molecule. If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig.
group: flexibility
explevel: expert
nseg15
default: -1
type: integer
title: Number of semi-flexible segments
min: -1
max: 1000
short description: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition).
long description: This parameter defines the number of semi-flexible segments for the specified molecule. If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig.
group: flexibility
explevel: expert
nseg16
default: -1
type: integer
title: Number of semi-flexible segments
min: -1
max: 1000
short description: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition).
long description: This parameter defines the number of semi-flexible segments for the specified molecule. If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig.
group: flexibility
explevel: expert
nseg17
default: -1
type: integer
title: Number of semi-flexible segments
min: -1
max: 1000
short description: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition).
long description: This parameter defines the number of semi-flexible segments for the specified molecule. If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig.
group: flexibility
explevel: expert
nseg18
default: -1
type: integer
title: Number of semi-flexible segments
min: -1
max: 1000
short description: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition).
long description: This parameter defines the number of semi-flexible segments for the specified molecule. If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig.
group: flexibility
explevel: expert
nseg19
default: -1
type: integer
title: Number of semi-flexible segments
min: -1
max: 1000
short description: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition).
long description: This parameter defines the number of semi-flexible segments for the specified molecule. If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig.
group: flexibility
explevel: expert
nseg2
default: -1
type: integer
title: Number of semi-flexible segments
min: -1
max: 1000
short description: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition).
long description: This parameter defines the number of semi-flexible segments for the specified molecule. If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig.
group: flexibility
explevel: expert
nseg20
default: -1
type: integer
title: Number of semi-flexible segments
min: -1
max: 1000
short description: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition).
long description: This parameter defines the number of semi-flexible segments for the specified molecule. If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig.
group: flexibility
explevel: expert
nseg3
default: -1
type: integer
title: Number of semi-flexible segments
min: -1
max: 1000
short description: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition).
long description: This parameter defines the number of semi-flexible segments for the specified molecule. If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig.
group: flexibility
explevel: expert
nseg4
default: -1
type: integer
title: Number of semi-flexible segments
min: -1
max: 1000
short description: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition).
long description: This parameter defines the number of semi-flexible segments for the specified molecule. If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig.
group: flexibility
explevel: expert
nseg5
default: -1
type: integer
title: Number of semi-flexible segments
min: -1
max: 1000
short description: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition).
long description: This parameter defines the number of semi-flexible segments for the specified molecule. If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig.
group: flexibility
explevel: expert
nseg6
default: -1
type: integer
title: Number of semi-flexible segments
min: -1
max: 1000
short description: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition).
long description: This parameter defines the number of semi-flexible segments for the specified molecule. If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig.
group: flexibility
explevel: expert
nseg7
default: -1
type: integer
title: Number of semi-flexible segments
min: -1
max: 1000
short description: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition).
long description: This parameter defines the number of semi-flexible segments for the specified molecule. If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig.
group: flexibility
explevel: expert
nseg8
default: -1
type: integer
title: Number of semi-flexible segments
min: -1
max: 1000
short description: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition).
long description: This parameter defines the number of semi-flexible segments for the specified molecule. If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig.
group: flexibility
explevel: expert
nseg9
default: -1
type: integer
title: Number of semi-flexible segments
min: -1
max: 1000
short description: This defines the number of semi-flexible segments (-1 automatic, 0 ridig, >1 manual definition).
long description: This parameter defines the number of semi-flexible segments for the specified molecule. If set to -1 then those are automatically defined based on contacts. Those can also be manually defined by defining the number of segment (nseg>=1). In that case the starting and ending residues of each segment must be defined. The position of atoms in regions outside the semi-flexible regions will have weak harmonic positional restraints during the energy minimisation. If nseg is set to 0, then the molecule will be kept ridig.
group: flexibility
explevel: expert
sampling_factor
default: 1
type: integer
title: Sampling factor for each starting model
min: 1
max: 500
short description: This parameter control how many times a model will be refined.
long description: This parameter control how many times a model will be refined. For EM refinement only it does not make sense to increase it unless random removal of restraints is turned on. If not then the energy minimisation will lead to the same final conformation.
group: sampling
explevel: expert
seg_end_10_1
default: nan
type: integer
title: Ending residue number
min: -9999
max: 9999
short description: Residue number defining the end of the semi-flexible segment.
long description: Residue number defining the end of the semi-flexible segment.
group: flexibility
explevel: expert
seg_end_11_1
default: nan
type: integer
title: Ending residue number
min: -9999
max: 9999
short description: Residue number defining the end of the semi-flexible segment.
long description: Residue number defining the end of the semi-flexible segment.
group: flexibility
explevel: expert
seg_end_12_1
default: nan
type: integer
title: Ending residue number
min: -9999
max: 9999
short description: Residue number defining the end of the semi-flexible segment.
long description: Residue number defining the end of the semi-flexible segment.
group: flexibility
explevel: expert
seg_end_13_1
default: nan
type: integer
title: Ending residue number
min: -9999
max: 9999
short description: Residue number defining the end of the semi-flexible segment.
long description: Residue number defining the end of the semi-flexible segment.
group: flexibility
explevel: expert
seg_end_14_1
default: nan
type: integer
title: Ending residue number
min: -9999
max: 9999
short description: Residue number defining the end of the semi-flexible segment.
long description: Residue number defining the end of the semi-flexible segment.
group: flexibility
explevel: expert
seg_end_15_1
default: nan
type: integer
title: Ending residue number
min: -9999
max: 9999
short description: Residue number defining the end of the semi-flexible segment.
long description: Residue number defining the end of the semi-flexible segment.
group: flexibility
explevel: expert
seg_end_16_1
default: nan
type: integer
title: Ending residue number
min: -9999
max: 9999
short description: Residue number defining the end of the semi-flexible segment.
long description: Residue number defining the end of the semi-flexible segment.
group: flexibility
explevel: expert
seg_end_17_1
default: nan
type: integer
title: Ending residue number
min: -9999
max: 9999
short description: Residue number defining the end of the semi-flexible segment.
long description: Residue number defining the end of the semi-flexible segment.
group: flexibility
explevel: expert
seg_end_18_1
default: nan
type: integer
title: Ending residue number
min: -9999
max: 9999
short description: Residue number defining the end of the semi-flexible segment.
long description: Residue number defining the end of the semi-flexible segment.
group: flexibility
explevel: expert
seg_end_19_1
default: nan
type: integer
title: Ending residue number
min: -9999
max: 9999
short description: Residue number defining the end of the semi-flexible segment.
long description: Residue number defining the end of the semi-flexible segment.
group: flexibility
explevel: expert
seg_end_1_1
default: nan
type: integer
title: Ending residue number
min: -9999
max: 9999
short description: Residue number defining the end of the semi-flexible segment.
long description: Residue number defining the end of the semi-flexible segment.
group: flexibility
explevel: expert
seg_end_20_1
default: nan
type: integer
title: Ending residue number
min: -9999
max: 9999
short description: Residue number defining the end of the semi-flexible segment.
long description: Residue number defining the end of the semi-flexible segment.
group: flexibility
explevel: expert
seg_end_2_1
default: nan
type: integer
title: Ending residue number
min: -9999
max: 9999
short description: Residue number defining the end of the semi-flexible segment.
long description: Residue number defining the end of the semi-flexible segment.
group: flexibility
explevel: expert
seg_end_3_1
default: nan
type: integer
title: Ending residue number
min: -9999
max: 9999
short description: Residue number defining the end of the semi-flexible segment.
long description: Residue number defining the end of the semi-flexible segment.
group: flexibility
explevel: expert
seg_end_4_1
default: nan
type: integer
title: Ending residue number
min: -9999
max: 9999
short description: Residue number defining the end of the semi-flexible segment.
long description: Residue number defining the end of the semi-flexible segment.
group: flexibility
explevel: expert
seg_end_5_1
default: nan
type: integer
title: Ending residue number
min: -9999
max: 9999
short description: Residue number defining the end of the semi-flexible segment.
long description: Residue number defining the end of the semi-flexible segment.
group: flexibility
explevel: expert
seg_end_6_1
default: nan
type: integer
title: Ending residue number
min: -9999
max: 9999
short description: Residue number defining the end of the semi-flexible segment.
long description: Residue number defining the end of the semi-flexible segment.
group: flexibility
explevel: expert
seg_end_7_1
default: nan
type: integer
title: Ending residue number
min: -9999
max: 9999
short description: Residue number defining the end of the semi-flexible segment.
long description: Residue number defining the end of the semi-flexible segment.
group: flexibility
explevel: expert
seg_end_8_1
default: nan
type: integer
title: Ending residue number
min: -9999
max: 9999
short description: Residue number defining the end of the semi-flexible segment.
long description: Residue number defining the end of the semi-flexible segment.
group: flexibility
explevel: expert
seg_end_9_1
default: nan
type: integer
title: Ending residue number
min: -9999
max: 9999
short description: Residue number defining the end of the semi-flexible segment.
long description: Residue number defining the end of the semi-flexible segment.
group: flexibility
explevel: expert
seg_sta_10_1
default: nan
type: integer
title: Starting residue number
min: -9999
max: 9999
short description: Residue number defining the start of the semi-flexible segment.
long description: Residue number defining the start of the semi-flexible segment.
group: flexibility
explevel: expert
seg_sta_11_1
default: nan
type: integer
title: Starting residue number
min: -9999
max: 9999
short description: Residue number defining the start of the semi-flexible segment.
long description: Residue number defining the start of the semi-flexible segment.
group: flexibility
explevel: expert
seg_sta_12_1
default: nan
type: integer
title: Starting residue number
min: -9999
max: 9999
short description: Residue number defining the start of the semi-flexible segment.
long description: Residue number defining the start of the semi-flexible segment.
group: flexibility
explevel: expert
seg_sta_13_1
default: nan
type: integer
title: Starting residue number
min: -9999
max: 9999
short description: Residue number defining the start of the semi-flexible segment.
long description: Residue number defining the start of the semi-flexible segment.
group: flexibility
explevel: expert
seg_sta_14_1
default: nan
type: integer
title: Starting residue number
min: -9999
max: 9999
short description: Residue number defining the start of the semi-flexible segment.
long description: Residue number defining the start of the semi-flexible segment.
group: flexibility
explevel: expert
seg_sta_15_1
default: nan
type: integer
title: Starting residue number
min: -9999
max: 9999
short description: Residue number defining the start of the semi-flexible segment.
long description: Residue number defining the start of the semi-flexible segment.
group: flexibility
explevel: expert
seg_sta_16_1
default: nan
type: integer
title: Starting residue number
min: -9999
max: 9999
short description: Residue number defining the start of the semi-flexible segment.
long description: Residue number defining the start of the semi-flexible segment.
group: flexibility
explevel: expert
seg_sta_17_1
default: nan
type: integer
title: Starting residue number
min: -9999
max: 9999
short description: Residue number defining the start of the semi-flexible segment.
long description: Residue number defining the start of the semi-flexible segment.
group: flexibility
explevel: expert
seg_sta_18_1
default: nan
type: integer
title: Starting residue number
min: -9999
max: 9999
short description: Residue number defining the start of the semi-flexible segment.
long description: Residue number defining the start of the semi-flexible segment.
group: flexibility
explevel: expert
seg_sta_19_1
default: nan
type: integer
title: Starting residue number
min: -9999
max: 9999
short description: Residue number defining the start of the semi-flexible segment.
long description: Residue number defining the start of the semi-flexible segment.
group: flexibility
explevel: expert
seg_sta_1_1
default: nan
type: integer
title: Starting residue number
min: -9999
max: 9999
short description: Residue number defining the start of the semi-flexible segment.
long description: Residue number defining the start of the semi-flexible segment.
group: flexibility
explevel: expert
seg_sta_20_1
default: nan
type: integer
title: Starting residue number
min: -9999
max: 9999
short description: Residue number defining the start of the semi-flexible segment.
long description: Residue number defining the start of the semi-flexible segment.
group: flexibility
explevel: expert
seg_sta_2_1
default: nan
type: integer
title: Starting residue number
min: -9999
max: 9999
short description: Residue number defining the start of the semi-flexible segment.
long description: Residue number defining the start of the semi-flexible segment.
group: flexibility
explevel: expert
seg_sta_3_1
default: nan
type: integer
title: Starting residue number
min: -9999
max: 9999
short description: Residue number defining the start of the semi-flexible segment.
long description: Residue number defining the start of the semi-flexible segment.
group: flexibility
explevel: expert
seg_sta_4_1
default: nan
type: integer
title: Starting residue number
min: -9999
max: 9999
short description: Residue number defining the start of the semi-flexible segment.
long description: Residue number defining the start of the semi-flexible segment.
group: flexibility
explevel: expert
seg_sta_5_1
default: nan
type: integer
title: Starting residue number
min: -9999
max: 9999
short description: Residue number defining the start of the semi-flexible segment.
long description: Residue number defining the start of the semi-flexible segment.
group: flexibility
explevel: expert
seg_sta_6_1
default: nan
type: integer
title: Starting residue number
min: -9999
max: 9999
short description: Residue number defining the start of the semi-flexible segment.
long description: Residue number defining the start of the semi-flexible segment.
group: flexibility
explevel: expert
seg_sta_7_1
default: nan
type: integer
title: Starting residue number
min: -9999
max: 9999
short description: Residue number defining the start of the semi-flexible segment.
long description: Residue number defining the start of the semi-flexible segment.
group: flexibility
explevel: expert
seg_sta_8_1
default: nan
type: integer
title: Starting residue number
min: -9999
max: 9999
short description: Residue number defining the start of the semi-flexible segment.
long description: Residue number defining the start of the semi-flexible segment.
group: flexibility
explevel: expert
seg_sta_9_1
default: nan
type: integer
title: Starting residue number
min: -9999
max: 9999
short description: Residue number defining the start of the semi-flexible segment.
long description: Residue number defining the start of the semi-flexible segment.
group: flexibility
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
w_air
default: 0.1
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: 0.0
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_elec
default: 0.2
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 EM 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: 1.0
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 EM 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
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