Refinements modules
[emref] module
Energy minimization refinement with CNS.
The [emref] module refines the input structure or a complex by energy minimization using
the conjugate gradient method implemented in CNS.
Coordinates of the energy-minimized structures are saved, and each structure/complex is then evaluated using HADDOCK scoring function.
The default HADDOCK scoring function in the [emref] module is the following:
Notable parameters
The most important parameters for the [emref] module are:
ambig_fname: file containing the ambiguous interaction restraints (AIRs, optional)unambig_fname: file containing the unambiguous interaction restraints (optional)randremoval: whether or not to activate the random removal of restraints (default: True)nemsteps: number of energy minimization steps (default: 200)
More information about the [emref] parameters is available here or retrieved by running:
haddock3-cfg -m emref
[flexref] module
Flexible refinement with CNS.
The [flexref] module (previously known as it1 stage in HADDOCK2.X series),
is a semi-flexible simulated annealing (SA) protocol based on molecular
dynamics (MD) in torsion angle space.
This semi-flexible SA consists of four sequential stages:
- High-temperature rigid body MD
- 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 are treated as semi-flexible. These regions are automatically defined based on intermolecular contacts. However, the user has the option to manually specify semi-flexible regions, and also define fully flexible regions that remain flexible throughout the entire protocol, starting from the high-temperature rigid-body MD stage.
See animation of the `[flexref]` protocol in action:
Here is a schematic visualization of the [flexref] stages with relevant parameters:
The temperature and number of steps for the various stages can be tuned.
The default HADDOCK scoring function in the [flexref] module is the following:
Notable parameters
The most important parameters for the [flexref] module are:
ambig_fname: file containing the ambiguous interaction restraints (AIRs, optional)unambig_fname: file containing the unambiguous interaction restraints (optional)seg_*_X_Y: for the definition of semi-flexible segments (see flexibility section for more information)fle_*_Y: for the definition of fully flexible segments (see flexibility section for more information)
More information about the [flexref] parameters is available here or retrieved by running:
haddock3-cfg -m flexref
[mdref] module
Explicit solvent MD refinement with CNS.
The [mdref] module (previously known as itw in HADDOCK2.X series), is a small MD simulation in cartesian space using explicit solvent.
A layer of solvent (8Å for water, 12.5Å for DMSO) is generated around surface residues.
The [mdref] protocol consists of four sequential steps:
- Short energy minimization
- Heating: 3 stages of short MD to reach the temperature of 300K (gradually increases the temperature, performing MD at 100K, 200K, and finally 300K)
- MD at 300K
- Cooling: 3 stages of short MD to reach the temperature of 100K (gradually decreases the temperature, performing MD at 300K, 200K, and finally 100K)
See animation of the `[mdref]` protocol in action:
Here is a schematic visualization of the [mdref] stages with relevant parameters:
Using this protocol with default parameters, no spectacular changes are expected;
however, the scoring of the various structures may be improved.
The default HADDOCK scoring function in the [mdref] module is the following:
Notable parameters
The most important parameters for the [mdref] module are:
ambig_fname: file containing the ambiguous interaction restraints (AIRs, optional)unambig_fname: file containing the unambiguous interaction restraints (optional)waterheatsteps: number of MD steps for heating up the system (default: 100)watersteps: number of MD steps at 300K (default: 1250)watercoolsteps: number of MD steps for cooling down the system (default: 500)
More information about [mdref] parameters is available here or retrieved by running:
haddock3-cfg -m mdref