Flexible refinement module

Module contents

Flexible refinement with CNS.

The [flexref] module (also known as it1 stage in HADDOCK2.X series), is a semi-flexible simulated annealing (SA) protocol based on molecular dynamics in torsion angle space.

This semi-flexible SA consists of several stages:

  • High temperature rigid body molecular dynamics

  • Rigid body SA

  • Semi-flexible SA with flexible side-chains at the interface

  • Semi-flexible SA with fully flexible interface (both backbone and side-chains)

By default, only the interface regions is treated as flexible. It is automatically defined based on the intermolecular contacts made. It is also possible to manually define the semi-flexible regions, and also define fully flexible regions that are allowed to move throughout the entire protocol from the high temperature rigid body molecular dynamics on.

The temperature and number of steps for the various stages can be tuned.

class haddock.modules.refinement.flexref.HaddockModule(order: int, path: Path, initial_params: str | Path = PosixPath('/opt/hostedtoolcache/Python/3.10.15/x64/lib/python3.10/site-packages/haddock/modules/refinement/flexref/defaults.yaml'))[source]

Bases: BaseCNSModule

HADDOCK3 module for flexible refinement.

classmethod confirm_installation() → None[source]

Confirm module is installed.

name: str = 'flexref'

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: 180
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

ligand_param_fname

default: ‘’
type: file
title: Custom ligand parameter file
short description: Ligand parameter file in CNS format
long description: Ligand parameter file in CNS format containing all force field parameters (bond, angles, dihedrals, impropers, van der waals) for any ligand not supported by default by HADDOCK
group: force field
explevel: easy

ligand_top_fname

default: ‘’
type: file
title: Custom ligand topology file
short description: Ligand topology file in CNS format
long description: Ligand topology file in CNS format containing the ligand topologies (atoms, masses, charges, bond definitions…) for any ligand not supported by default by HADDOCK
group: force field
explevel: easy

mol_shape_1

default: False
type: boolean
title: Is the molecule a shape?
short description: Defines a molecule as a shape.
long description: Defines a molecule as a shape, which is a collection of beads.
group: molecule
explevel: easy

sinter_rigid_final

default: 0.001
type: float
title: End rigid-body MD intermolecular interactions scaling factor.
min: 1e-05
max: 1
short description: End scaling factor for intermolecular interactions in the first cooling stage.
long description: End scaling factor applied to intermolecular interactions during the first cooling stage of the simulated annealing protocol.
group: sampling
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

ambig_cool1

default: 10
type: integer
title: First cooling SA force constant for ambiguous distance restraints
min: 0
max: 1000
short description: Force constant applied to the distance restraints defined in ambig_fname during the first cooling phase of the SA.
long description: Force constant applied to the distance restraints defined in ambig_fname during the first cooling phase of the simulatd annealing protocol. Molecules are treated as rigid bodies unless fully flexible segments are defined (see nfle parameter).
group: distance restraints
explevel: expert

ambig_cool2

default: 50
type: integer
title: Second cooling SA force constant for ambiguous distance restraints
min: 0
max: 1000
short description: Force constant applied to the distance restraints defined in ambig_fname during the second cooling phase of the SA.
long description: Force constant applied to the distance restraints defined in ambig_fname during the second cooling phase of the simulatd annealing protocol. Side-chains at the interface are treated as flexible and any region defined in fully flexible segments as fully flexible (see nfle parameter).
group: distance restraints
explevel: expert

ambig_cool3

default: 50
type: integer
title: Third cooling SA force constant for ambiguous distance restraints
min: 0
max: 1000
short description: Force constant applied to the distance restraints defined in ambig_fname during the third cooling phase of the SA.
long description: Force constant applied to the distance restraints defined in ambig_fname during the third cooling phase of the simulatd annealing protocol. Side-chains and backbone at the interface are treated as flexible and any region defined in fully flexible segments as fully flexible (see nfle parameter).
group: distance restraints
explevel: expert

ambig_hot

default: 10
type: integer
title: Hot phase SA force constant for ambiguous distance restraints
min: 0
max: 1000
short description: Force constant applied to the distance restraints defined in ambig_fname during the hot phase of the SA.
long description: Force constant applied to the distance restraints defined in ambig_fname during the initial hot phase of the simulatd annealing protocol. Molecules are treated as rigid bodies unless fully flexible segments are defined (see nfle parameter).
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: ‘rdie’
type: string
title: Constant (cdie) or distance-dependent dielectric (rdie) constant.
choices: [‘cdie’, ‘rdie’]
short description: Use a constant (cdie option) or a distance-dependent dielectric (rdie) constant in the Coulomb potential.
long description: Use a constant (cdie option) or a distance-dependent dielectric (rdie) constant in the Coulomb potential. A distance dependent dielectric constant will effectively scale down the electrostatic energy by having a 1/r**2 dependency instead of 1/r
group: force field
explevel: expert

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_cool1

default: 5
type: integer
title: First cooling SA force constant for dihedral angle restraints
min: 0
max: 1000
short description: First cooling SA force constant for dihedral angle restraints read from dihe_fname.
long description: Force constant applied to the dihedral angle restraints read from dihe_fname during the first cooling phase of the simulatd annealing protocol.
group: dihedral restraints
explevel: expert

dihedrals_cool2

default: 50
type: integer
title: Second cooling SA force constant for dihedral angle restraints
min: 0
max: 1000
short description: Second cooling SA force constant for dihedral angle restraints read from dihe_fname.
long description: Force constant applied to the dihedral angle restraints read from dihe_fname during the second cooling phase of the simulatd annealing protocol.
group: dihedral restraints
explevel: expert

dihedrals_cool3

default: 200
type: integer
title: Third cooling SA force constant for dihedral angle restraints
min: 0
max: 1000
short description: Third cooling SA force constant for dihedral angle restraints read from dihe_fname.
long description: Force constant applied to the dihedral angle restraints read from dihe_fname during the third cooling phase of the simulatd annealing protocol.
group: dihedral restraints
explevel: expert

dihedrals_hot

default: 5
type: integer
title: Hot phase SA force constant for dihedral angle restraints
min: 0
max: 1000
short description: Hot phase SA force constant for dihedral angle restraints read from dihe_fname.
long description: Force constant applied to the dihedral angle restraints read from dihe_fname during the initial hot phase of the simulatd annealing protocol.
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_1

default: nan
type: integer
title: End residue number
min: -9999
max: 9999
short description: Residue number defining the end of the fully flexible segment.
long description: Residue number defining the end of this (1st) fully flexible segment.
group: flexibility
explevel: expert

fle_seg_1

default: ‘none’
type: string
title: Segment ID (segid)
short description: Segment ID of the molecule for which this flexible segment is defined.
long description: Segment ID of the molecule for which this (1st) flexible segment is defined.
group: flexibility
explevel: expert

fle_sta_1

default: nan
type: integer
title: Starting residue number
min: -9999
max: 9999
short description: Residue number defining the start of the fully flexible segment.
long description: Residue number defining the start of this (1st) fully flexible segment.
group: flexibility
explevel: expert

hbond_cool1

default: 10
type: integer
title: Hot phase SA force constant for hydrogen bond restraints
min: 0
max: 1000
short description: Force constant applied to the hydrogen bond restraints defined in hbond_fname during the hot phase of the SA.
long description: Force constant applied to the hydrogen bond restraints defined in hbond_fname during the initial hot phase of the simulatd annealing protocol. Molecules are treated as rigid bodies unless fully flexible segments are defined (see nfle parameter).
group: distance restraints
explevel: expert

hbond_cool2

default: 50
type: integer
title: Hot phase SA force constant for hydrogen bond restraints
min: 0
max: 1000
short description: Force constant applied to the hydrogen bond restraints defined in hbond_fname during the hot phase of the SA.
long description: Force constant applied to the hydrogen bond restraints defined in hbond_fname during the initial hot phase of the simulatd annealing protocol. Molecules are treated as rigid bodies unless fully flexible segments are defined (see nfle parameter).
group: distance restraints
explevel: expert

hbond_cool3

default: 50
type: integer
title: Hot phase SA force constant for hydrogen bond restraints
min: 0
max: 1000
short description: Force constant applied to the hydrogen bond restraints defined in hbond_fname during the hot phase of the SA.
long description: Force constant applied to the hydrogen bond restraints defined in hbond_fname during the initial hot phase of the simulatd annealing protocol. Molecules are treated as rigid bodies unless fully flexible segments are defined (see nfle parameter).
group: distance restraints
explevel: expert

hbond_hot

default: 10
type: integer
title: Hot phase SA force constant for hbond distance restraints
min: 0
max: 1000
short description: Force constant applied to the hydrogen bond restraints defined in hbond_fname during the hot phase of the SA.
long description: Force constant applied to the hydrogen bond restraints defined in hbond_fname during the initial hot phase of the simulatd annealing protocol. Molecules are treated as rigid bodies unless fully flexible segments are defined (see nfle parameter).
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

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

mdsteps_cool1

default: 500
type: integer
title: First cooling phase SA MD steps
min: 0
max: 10000
short description: Number of MD steps for the first cooling phase of the SA.
long description: Number of MD steps for the first cooling phase of rigid body dynamics of the simulated annealing protocol.
group: sampling
explevel: expert

mdsteps_cool2

default: 1000
type: integer
title: Second cooling phase SA MD steps
min: 0
max: 10000
short description: Number of MD steps for the second cooling phase of the SA.
long description: Number of MD steps for the second cooling phase of torsion angle dynamics of the simulated annealing protocol with flexible side-chains at the interface. Full flexibility is applied to the segments defined as fully flexible (see nfle and related parameters).
group: sampling
explevel: expert

mdsteps_cool3

default: 1000
type: integer
title: Third cooling phase SA MD steps
min: 0
max: 10000
short description: Number of MD steps for the third cooling phase of the SA.
long description: Number of MD steps for the third cooling phase of torsion angle dynamics of the simulated annealing protocol with flexible side-chains and backbone at the interface. Full flexibility is applied to the segments defined as fully flexible (see nfle and related parameters).
group: sampling
explevel: expert

mdsteps_rigid

default: 500
type: integer
title: Hot phase SA MD steps
min: 0
max: 10000
short description: Number of MD steps for the hot phase of the SA.
long description: Number of MD steps for the hot phase rigid body dynamics of the simulated annealing protocol.
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

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

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: 500
short description: This paramater controls how many times a model will be refined.
long description: This paramater controls 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

unambig_cool1

default: 10
type: integer
title: Hot phase SA force constant for unambiguous distance restraints
min: 0
max: 1000
short description: Force constant applied to the distance restraints defined in unambig_fname during the hot phase of the SA.
long description: Force constant applied to the distance restraints defined in unambig_fname during the initial hot phase of the simulatd annealing protocol. Molecules are treated as rigid bodies unless fully flexible segments are defined (see nfle parameter).
group: distance restraints
explevel: expert

unambig_cool2

default: 50
type: integer
title: Hot phase SA force constant for unambiguous distance restraints
min: 0
max: 1000
short description: Force constant applied to the distance restraints defined in ambig_fname during the hot phase of the SA.
long description: Force constant applied to the distance restraints defined in unambig_fname during the initial hot phase of the simulatd annealing protocol. Molecules are treated as rigid bodies unless fully flexible segments are defined (see nfle parameter).
group: distance restraints
explevel: expert

unambig_cool3

default: 50
type: integer
title: Hot phase SA force constant for unambiguous distance restraints
min: 0
max: 1000
short description: Force constant applied to the distance restraints defined in unambig_fname during the hot phase of the SA.
long description: Force constant applied to the distance restraints defined in unambig_fname during the initial hot phase of the simulatd annealing protocol. Molecules are treated as rigid bodies unless fully flexible segments are defined (see nfle parameter).
group: distance restraints
explevel: expert

unambig_hot

default: 10
type: integer
title: Hot phase SA force constant for unambiguous distance restraints
min: 0
max: 1000
short description: Force constant applied to the distance restraints defined in unambig_fname during the hot phase of the SA.
long description: Force constant applied to the distance restraints defined in unambig_fname during the initial hot phase of the simulatd annealing protocol. Molecules are treated as rigid bodies unless fully flexible segments are defined (see nfle parameter).
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: -0.01
type: float
title: Weight of the buried surface area term
min: -9999
max: 9999
short description: Weight of the buried surface area term in the scoring function
long description: Weight of the buried surface area (BSA) term in the scoring function. Note that the BSA is only used for scoring.
group: scoring
explevel: expert

w_cdih

default: 0.0
type: float
title: Weight of the dihedral angle restraint energy
min: 0
max: 9999
short description: Weight of the dihedral angle restraints energy in the scoring function
long description: Weight of the dihedral angle restraints energy in the scoring function. Note that this is different from the force constant used during the calculations.
group: scoring
explevel: expert

w_desolv

default: 1.0
type: float
title: Weight of the desolvation energy term
min: -9999
max: 9999
short description: Weight of the desolvation energy term in the scoring function
long description: Weight of the desolvation energy term in the scoring function. Note that the desolvation energy is only used for scoring.
group: scoring
explevel: expert

w_elec

default: 1.0
type: float
title: Weight of the intermolecular electrostatic energy
min: -9999
max: 9999
short description: Weight of the intermolecular electrostatic energy in the scoring function
long description: Weight of the intermolecular electrostatic energy in the scoring function. Note that this does not affect the electostatic energy during the 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

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

randorien

default: False
type: boolean
title: Randomize starting orientations
short description: Randomize starting orientations
long description: Randomize starting orientations by separating the molecules in space and randomly rotating those
group: sampling
explevel: guru

sinter_cool2_final

default: 1.0
type: float
title: End intermolecular interactions scaling factor for the 2nd cooling phase.
min: 1e-05
max: 1
short description: End scaling factor for intermolecular interactions in the second MD cooling SA stage.
long description: End scaling factor applied to intermolecular interactions during the second torsion angle molecular dynamics cooling stage of the simulated annealing protocol during which side-chains at the interface are treated as flexible.
group: sampling
explevel: guru

sinter_cool2_init

default: 0.001
type: float
title: Initial intermolecular interactions scaling factor for the 2nd cooling phase.
min: 1e-05
max: 1
short description: Initial scaling factor for intermolecular interactions in the second MD cooling SA stage.
long description: Initial scaling factor applied to intermolecular interactions during the second torsion angle molecular dynamics cooling stage of the simulated annealing protocol during which side-chains at the interface are treated as flexible.
group: sampling
explevel: guru

sinter_cool3_final

default: 1.0
type: float
title: End intermolecular interactions scaling factor for the 3rd cooling phase.
min: 1e-05
max: 1
short description: End scaling factor for intermolecular interactions in the third MD cooling SA stage.
long description: End scaling factor applied to intermolecular interactions during the third and final torsion angle molecular dynamics cooling stage of the simulated annealing protocol during which both side-chains and backbone at the interface are treated as flexible.
group: sampling
explevel: guru

sinter_cool3_init

default: 0.05
type: float
title: Initial intermolecular interactions scaling factor for the 3rd cooling phase.
min: 1e-05
max: 1
short description: Initial scaling factor for intermolecular interactions in the third MD cooling SA stage.
long description: Initial scaling factor applied to intermolecular interactions during the third and final torsion angle molecular dynamics cooling stage of the simulated annealing protocol during which both side-chains and backbone at the interface are treated as flexible.
group: sampling
explevel: guru

sinter_rigid_init

default: 0.001
type: float
title: Initial rigid-body MD intermolecular interactions scaling factor.
min: 1e-05
max: 1
short description: Initial scaling factor for intermolecular interactions in the first two SA stages
long description: Initial scaling factor applied to intermolecular interactions during the first rigid-body molecular dynamics stage and at the start of the first cooling stage of the of the simulated annealing protocol.
group: sampling
explevel: guru

tadfactor

default: 8
type: integer
title: Scaling factor for the integration time step.
min: 1
max: 10
short description: Initial scaling factor for the integration time step of the hot phase SA.
long description: Scaling factor applied at the start of the simulated annealing protocol to the timestep using during torsion angle molecular dynamics. This factor is automatically reduced during the SA protocol.
group: sampling
explevel: guru

temp_cool1_final

default: 500
type: integer
title: End temperature for the 1st cooling phase
min: 1
max: 1000
short description: End temperature for the first rigid-body MD cooling phase in Kelvin.
long description: End temperature in Kelvin for the first rigid-body molecular dynamic cooling phase of the simulated annealing protocol.
group: sampling
explevel: guru

temp_cool1_init

default: 2000
type: integer
title: Start temperature for the 1st cooling phase
min: 1
max: 5000
short description: Starting temperature for the first rigid-body MD cooling phase in Kelvin.
long description: Starting temperature in Kelvin for the first rigid-body molecular dynamic cooling phase of the simulated annealing protocol.
group: sampling
explevel: guru

temp_cool2_final

default: 50
type: integer
title: End temperature for the 2nd cooling phase
min: 1
max: 1000
short description: End temperature for the second MD cooling phase in Kelvin.
long description: End temperature in Kelvin for the second torsion angle molecular dynamic cooling phase of the simulated annealing protocol in which side-chains at the interface are treated as flexible.
group: sampling
explevel: guru

temp_cool2_init

default: 1000
type: integer
title: Start temperature for the 2nd cooling phase
min: 1
max: 2000
short description: Starting temperature for the second MD cooling phase in Kelvin.
long description: Starting temperature in Kelvin for the second torsion angle molecular dynamic cooling phase of the simulated annealing protocol in which side-chains at the interface are treated as flexible.
group: sampling
explevel: guru

temp_cool3_final

default: 50
type: integer
title: End temperature for the 3rd cooling phase
min: 1
max: 1000
short description: End temperature for the third MD cooling phase in Kelvin.
long description: End temperature in Kelvin for the third and final torsion angle molecular dynamic cooling phase of the simulated annealing protocol in which side-chains and backbone at the interface are treated as flexible.
group: sampling
explevel: guru

temp_cool3_init

default: 1000
type: integer
title: Start temperature for the 3rd cooling phase
min: 1
max: 1000
short description: Starting temperature for the third MD cooling phase in Kelvin.
long description: Starting temperature in Kelvin for the third and final torsion angle molecular dynamic cooling phase of the simulated annealing protocol in which side-chains and backbone at the interface are treated as flexible.
group: sampling
explevel: guru

temp_high

default: 2000
type: integer
title: Initial rigid-body MD temperature
min: 1
max: 5000
short description: Temperature for the initial rigid-body MD phase in Kelvin.
long description: Temperature in Kelvin for the initial rigid-body molecular dynamic phase of the simulated annealing protocol.
group: sampling
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 torsion angle molecular dynamics.
long description: Integration time step for the torsion angle molecular dynamics.
group: sampling
explevel: guru