Water refinement module

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

dihe_fname

default: ‘’
type: file
title: Dihedral angle restraints filename
short description: Filename of the Dihedral angle restraints file
long description: Filename of the Dihedral angle restraints file.
group: dihedral restraints
explevel: easy

dihedrals_on

default: False
type: boolean
title: Use dihedral angle restraints
short description: Turns on dihedral angle restraints.
long description: Turns on dihedral angle restraints. Those should be defined in the dihe_fname file.
group: dihedral restraints
explevel: easy

dnarest_on

default: False
type: boolean
title: Restrain the DNA conformation
short description: Automatically creates restraints to maintain the conformation of DNA/RNA
long description: This option allows to restraint the conformation of nucleic acids based on the values from the input structures. The following restraints will be automatically defined: - single base planarity - sugar pucker - phosphate backbone diherdral angle restraints - Watson-Crick base pairing
group: other 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

error_dih

default: 10
type: integer
title: Force constant for backbone dihedral angle restraints
min: 0
max: 1000
short description: Force constant for backbone dihedral angle restraints (ssdihed option)
long description: Force constant for backbone dihedral angle restraints (ssdihed option)
group: dihedral restraints
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

solvent

default: ‘water’
type: string
title: Solvent
choices: [‘water’, ‘dmso’]
short description: Solvent to use during the short MD refinement
long description: Solvent to use during the short MD refinement. Water and DMSO are supported. A solvent shelll is generated by shifting pre-equilibrated boxes around the complex. For water an 8A water shell is generated and for DMSO a 12.5A shell. For DMSO,
group:
explevel: easy

ssdihed

default: ‘none’
type: string
title: Define automatically backbone dihedral angle restraints
choices: [‘none’, ‘all’, ‘alpha’, ‘alphabeta’]
short description: If turned on, this option will automatically defined backbone dihedral angle restraints for the selected regions.
long description: This option allows to utomatically defined backbone dihedral angle restraints for the selected regions. The restraints will be defined for the phi and psi backbone dihedral angles of amino acids, with the target value taken from the measured angle in the input structure, and the error bound defined by the error_dih parameter. Those restraints can be applied to the entire structure (all), the alpha/beta secondary structure elements (alphabeta) or only to the alpha helical regions (alpha). Those are automatically detected based on the measured dihedral angle combinations.
group: dihedral restraints
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

amb_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: distance restraints
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: distance restraints
explevel: expert

contactairs

default: False
type: boolean
title: Contact restraints
short description: Contact restraints between molecules
long description: Contact restraints between molecules. These are defined as ambiguous distance restraint between each residue of a molecule and all residues of the other molecules with 5A from that residue. This can be used to restraint the contacts between the interfaces. Note that this can generate a large number of ambiguous restraints and slow down the computations
group: distance restraints
explevel: 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

dihedrals_scale

default: 200
type: integer
title: Force constant for dihedral angle restraints
min: 0
max: 1000
short description: Force constant applied to the dihedral angle restraints read from dihe_fname.
long description: Force constant applied to the dihedral angle restraints read from dihe_fname.
group: dihedral restraints
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

fle_end_10_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 the fully flexible segment.
group: flexibility
explevel: expert

fle_end_11_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 the fully flexible segment.
group: flexibility
explevel: expert

fle_end_12_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 the fully flexible segment.
group: flexibility
explevel: expert

fle_end_13_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 the fully flexible segment.
group: flexibility
explevel: expert

fle_end_14_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 the fully flexible segment.
group: flexibility
explevel: expert

fle_end_15_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 the fully flexible segment.
group: flexibility
explevel: expert

fle_end_16_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 the fully flexible segment.
group: flexibility
explevel: expert

fle_end_17_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 the fully flexible segment.
group: flexibility
explevel: expert

fle_end_18_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 the fully flexible segment.
group: flexibility
explevel: expert

fle_end_19_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 the fully flexible segment.
group: flexibility
explevel: expert

fle_end_1_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 the fully flexible segment.
group: flexibility
explevel: expert

fle_end_20_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 the fully flexible segment.
group: flexibility
explevel: expert

fle_end_2_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 the fully flexible segment.
group: flexibility
explevel: expert

fle_end_3_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 the fully flexible segment.
group: flexibility
explevel: expert

fle_end_4_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 the fully flexible segment.
group: flexibility
explevel: expert

fle_end_5_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 the fully flexible segment.
group: flexibility
explevel: expert

fle_end_6_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 the fully flexible segment.
group: flexibility
explevel: expert

fle_end_7_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 the fully flexible segment.
group: flexibility
explevel: expert

fle_end_8_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 the fully flexible segment.
group: flexibility
explevel: expert

fle_end_9_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 the fully flexible segment.
group: flexibility
explevel: expert

fle_sta_10_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 the fully flexible segment.
group: flexibility
explevel: expert

fle_sta_11_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 the fully flexible segment.
group: flexibility
explevel: expert

fle_sta_12_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 the fully flexible segment.
group: flexibility
explevel: expert

fle_sta_13_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 the fully flexible segment.
group: flexibility
explevel: expert

fle_sta_14_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 the fully flexible segment.
group: flexibility
explevel: expert

fle_sta_15_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 the fully flexible segment.
group: flexibility
explevel: expert

fle_sta_16_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 the fully flexible segment.
group: flexibility
explevel: expert

fle_sta_17_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 the fully flexible segment.
group: flexibility
explevel: expert

fle_sta_18_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 the fully flexible segment.
group: flexibility
explevel: expert

fle_sta_19_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 the fully flexible segment.
group: flexibility
explevel: expert

fle_sta_1_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 the fully flexible segment.
group: flexibility
explevel: expert

fle_sta_20_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 the fully flexible segment.
group: flexibility
explevel: expert

fle_sta_2_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 the fully flexible segment.
group: flexibility
explevel: expert

fle_sta_3_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 the fully flexible segment.
group: flexibility
explevel: expert

fle_sta_4_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 the fully flexible segment.
group: flexibility
explevel: expert

fle_sta_5_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 the fully flexible segment.
group: flexibility
explevel: expert

fle_sta_6_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 the fully flexible segment.
group: flexibility
explevel: expert

fle_sta_7_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 the fully flexible segment.
group: flexibility
explevel: expert

fle_sta_8_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 the fully flexible segment.
group: flexibility
explevel: expert

fle_sta_9_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 the fully flexible segment.
group: flexibility
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

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: distance restraints
explevel: expert

kcont

default: 1.0
type: float
title: Contact restraints force constant
min: 0
max: 1000
short description: Force constant applied to the contact restraints.
long description: Force constant applied to the contact restraints.
group: distance restraints
explevel: expert

kncs

default: 1.0
type: float
title: Force constant for non-crystallographic restraints
min: 0
max: 1000
short description: Force constant for non-crystallographic restraints
long description: Force constant for non-crystallographic restraints
group: symmetry
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

max_nmodels

default: 10000
type: integer
title: Maximum number of models to refine
min: 1
max: 50000
short description: This paramater controls the maximum number of models to refine.
long description: This paramater 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

ncs_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 NCS segment
long description: Residue number of last residue in the first NCS segment
group: symmetry
explevel: expert

ncs_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 NCS segment
long description: Residue number of last residue in the second NCS segment
group: symmetry
explevel: expert

ncs_on

default: False
type: boolean
title: Non-crystallographic symmetry restraints
short description: Non-crystallographic symmetry restraints to ensure two molecules will have the same conformation.
long description: Non-crystallographic symmetry restraints to ensure two molecules will have the same conformation. This does not apply any symmetry between the two molecules but rather defines restraints such as the RMSD between those is 0.
group: symmetry
explevel: expert

ncs_seg1_1

default: ‘’
type: string
title: Segment ID of first NCS segment
short description: Segment ID of first NCS segment
long description: Segment ID of first NCS segment
group: symmetry
explevel: expert

ncs_seg2_1

default: ‘’
type: string
title: Segment ID of second NCS segment
short description: Segment ID of second NCS segment
long description: Segment ID of second NCS segment
group: symmetry
explevel: expert

ncs_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 NCS segment
long description: Residue number of first residue in the first NCS segment
group: symmetry
explevel: expert

ncs_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 NCS segment
long description: Residue number of first residue in the second NCS segment
group: symmetry
explevel: expert

nemsteps

default: 200
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 in the various EM stages of this refinement protocol. Note that the effective number might be smaller if the minimisation converges earlier.
group: sampling
explevel: expert

nfle1

default: 0
type: integer
title: Number of fully flexible segments
min: 0
max: 1000
short description: This defines the number of fully flexible segments.
long description: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.
group: flexibility
explevel: expert

nfle10

default: 0
type: integer
title: Number of fully flexible segments
min: 0
max: 1000
short description: This defines the number of fully flexible segments.
long description: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.
group: flexibility
explevel: expert

nfle11

default: 0
type: integer
title: Number of fully flexible segments
min: 0
max: 1000
short description: This defines the number of fully flexible segments.
long description: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.
group: flexibility
explevel: expert

nfle12

default: 0
type: integer
title: Number of fully flexible segments
min: 0
max: 1000
short description: This defines the number of fully flexible segments.
long description: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.
group: flexibility
explevel: expert

nfle13

default: 0
type: integer
title: Number of fully flexible segments
min: 0
max: 1000
short description: This defines the number of fully flexible segments.
long description: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.
group: flexibility
explevel: expert

nfle14

default: 0
type: integer
title: Number of fully flexible segments
min: 0
max: 1000
short description: This defines the number of fully flexible segments.
long description: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.
group: flexibility
explevel: expert

nfle15

default: 0
type: integer
title: Number of fully flexible segments
min: 0
max: 1000
short description: This defines the number of fully flexible segments.
long description: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.
group: flexibility
explevel: expert

nfle16

default: 0
type: integer
title: Number of fully flexible segments
min: 0
max: 1000
short description: This defines the number of fully flexible segments.
long description: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.
group: flexibility
explevel: expert

nfle17

default: 0
type: integer
title: Number of fully flexible segments
min: 0
max: 1000
short description: This defines the number of fully flexible segments.
long description: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.
group: flexibility
explevel: expert

nfle18

default: 0
type: integer
title: Number of fully flexible segments
min: 0
max: 1000
short description: This defines the number of fully flexible segments.
long description: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.
group: flexibility
explevel: expert

nfle19

default: 0
type: integer
title: Number of fully flexible segments
min: 0
max: 1000
short description: This defines the number of fully flexible segments.
long description: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.
group: flexibility
explevel: expert

nfle2

default: 0
type: integer
title: Number of fully flexible segments
min: 0
max: 1000
short description: This defines the number of fully flexible segments.
long description: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.
group: flexibility
explevel: expert

nfle20

default: 0
type: integer
title: Number of fully flexible segments
min: 0
max: 1000
short description: This defines the number of fully flexible segments.
long description: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.
group: flexibility
explevel: expert

nfle3

default: 0
type: integer
title: Number of fully flexible segments
min: 0
max: 1000
short description: This defines the number of fully flexible segments.
long description: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.
group: flexibility
explevel: expert

nfle4

default: 0
type: integer
title: Number of fully flexible segments
min: 0
max: 1000
short description: This defines the number of fully flexible segments.
long description: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.
group: flexibility
explevel: expert

nfle5

default: 0
type: integer
title: Number of fully flexible segments
min: 0
max: 1000
short description: This defines the number of fully flexible segments.
long description: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.
group: flexibility
explevel: expert

nfle6

default: 0
type: integer
title: Number of fully flexible segments
min: 0
max: 1000
short description: This defines the number of fully flexible segments.
long description: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.
group: flexibility
explevel: expert

nfle7

default: 0
type: integer
title: Number of fully flexible segments
min: 0
max: 1000
short description: This defines the number of fully flexible segments.
long description: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.
group: flexibility
explevel: expert

nfle8

default: 0
type: integer
title: Number of fully flexible segments
min: 0
max: 1000
short description: This defines the number of fully flexible segments.
long description: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.
group: flexibility
explevel: expert

nfle9

default: 0
type: integer
title: Number of fully flexible segments
min: 0
max: 1000
short description: This defines the number of fully flexible segments.
long description: This parameter defines the number of fully flexible segments for the specified molecule. If >=1 then those must be defined manually with starting and end residue numbers in the fle_sta_* and fle_end_* variables.
group: flexibility
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

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

numc2sym

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

numc3sym

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

numc4sym

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

numc5sym

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

numc6sym

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

numncs

default: 0
type: integer
title: Number of non-crystallographic symmetry restraints
min: 0
max: 100
short description: Number of non-crystallographic symmetry restraints (NCS).
long description: Number of non-crystallographic symmetry restraints. For each pairs of segments will have to be defined. Note that those must contain exactly the same residues/atom combinations.
group: symmetry
explevel: expert

nums3sym

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

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

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

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

sampling_factor

default: 1
type: integer
title: Sampling factor for each starting model
min: 1
max: 200
short description: This paramater control how many times a model will be refined.
long description: This paramater control how many times a model will be refined.
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

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

unamb_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: 0.1
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 MD refinement.
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 MD refinement.
group: scoring
explevel: expert

watercoolsteps

default: 500
type: integer
title: Number of MD steps for the cooling
min: 0
max: 10000
short description: Number of MD steps for the cooling phase.
long description: Number of MD steps for the cooling phase. The cooling consists of three successive short molecular dynamics simluations at 300, 200 and 100 Kelvin.
group: sampling
explevel: expert

waterheatsteps

default: 100
type: integer
title: Number of MD steps for the heating
min: 0
max: 10000
short description: Number of MD steps for the heating phase.
long description: Number of MD steps for the heating phase. The heating consists of three successive short molecular dynamics simluations at 100, 200 and 300 Kelvin.
group: sampling
explevel: expert

watersteps

default: 1250
type: integer
title: Number of MD steps at 300K.
min: 0
max: 100000
short description: Number of MD steps for 300K simulation.
long description: Number of MD steps for 300K simulation. This is the sampling state of the refinement.
group: sampling
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

timestep

default: 0.002
type: float
title: MD integrating time step
min: 0.0005
max: 0.004
short description: Integration time step for the molecular dynamics.
long description: Integration time step for the molecular dynamics.
group: sampling
explevel: guru

Water refinement module

Module contents

Default Parameters

Easy

ambig_fname

dihe_fname

dihedrals_on

dnarest_on

elecflag

error_dih

hbond_fname

mol_shape_1

solvent

ssdihed

unambig_fname

Expert

amb_scale

c2sym_end1_1

c2sym_end2_1

c2sym_seg1_1

c2sym_seg2_1

c2sym_sta1_1

c2sym_sta2_1

c3sym_end1_1

c3sym_end2_1

c3sym_end3_1

c3sym_seg1_1

c3sym_seg2_1

c3sym_seg3_1

c3sym_sta1_1

c3sym_sta2_1

c3sym_sta3_1

c4sym_end1_1

c4sym_end2_1

c4sym_end3_1

c4sym_end4_1

c4sym_seg1_1

c4sym_seg2_1

c4sym_seg3_1

c4sym_seg4_1

c4sym_sta1_1

c4sym_sta2_1

c4sym_sta3_1

c4sym_sta4_1

c5sym_end1_1

c5sym_end2_1

c5sym_end3_1

c5sym_end4_1

c5sym_end5_1

c5sym_seg1_1

c5sym_seg2_1

c5sym_seg3_1

c5sym_seg4_1

c5sym_seg5_1

c5sym_sta1_1

c5sym_sta2_1

c5sym_sta3_1

c5sym_sta4_1

c5sym_sta5_1

c6sym_end1_1

c6sym_end2_1

c6sym_end3_1

c6sym_end4_1

c6sym_end5_1

c6sym_end6_1

c6sym_seg1_1

c6sym_seg2_1

c6sym_seg3_1

c6sym_seg4_1

c6sym_seg5_1

c6sym_seg6_1

c6sym_sta1_1

c6sym_sta2_1

c6sym_sta3_1

c6sym_sta4_1

c6sym_sta5_1

c6sym_sta6_1

cmrest

cmtight

contactairs