Molecular Dynamics scoring module
Module contents
MD scoring module.
This module will perform a short MD simulation on the input models and score them. No restraints are applied during this step.
- class haddock.modules.scoring.mdscoring.HaddockModule(order: int, path: Path, initial_params: str | Path = PosixPath('/opt/hostedtoolcache/Python/3.10.15/x64/lib/python3.10/site-packages/haddock/modules/scoring/mdscoring/defaults.yaml'))[source]
Bases:
CNSScoringModuleHADDOCK3 module to perform energy minimization scoring.
Default Parameters
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
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
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
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
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
individualize
default: True
type: boolean
title: Individualise models
short description: Treat each model in the PDB ensemble as a separate entity.
long description: Treat each model in the PDB ensemble as a separate entity. This means that for each a separate topology file will be generated. The models in the ensemble can thus correspond to different molecules.
group: sampling
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
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
per_interface_scoring
default: False
type: boolean
title: Interchain scoring
short description: Output scores per interface in the PDB header.
long description: With this option true, the interface of all combinations of chains will be analysed and the corresponding HADDOCK scores (without restraints terms) and their components (Eelec, Evdw, Edesol, BSA) will be written to the header of each PDB file.
group: scoring
explevel: expert
tolerance
default: 5
type: integer
title: Failure tolerance percentage
min: 0
max: 99
short description: Percentage of allowed failures for a module to successfully complete
long description: Percentage of allowed failures for a module to successfully complete
group: module
explevel: expert
w_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_vdw
default: 1.0
type: float
title: Weight of the intermolecular van der Waals energy
min: -9999
max: 9999
short description: Weight of the intermolecular van der Waals energy in the scoring function
long description: Weight of the intermolecular van der Waals energy in the scoring function. Note that this does not affect the van der Waals energy during the EM minimization.
group: scoring
explevel: expert
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