Topology modules

[topoaa] module

The [topoaa] module is dedicated to the generation of CNS compatible parameters (.param) and topologies (.psf) for each of the input structures.

It will:

  • Detect missing atoms, including hydrogens
  • Re-build them when missing
  • Build and write out topologies (.psf) and coordinates (.pdb) files

This module is a prerequisite to run any downstream modules using CNS. Having access to parameters and topology is mandatory for any kind of EM/MD related tasks. Therefore this is the reason why the module [topoaa] is often used as first module in a workflow.

Note that for non-standard bio-molecules (apart from standard amino-acids, some modified ones, DNA, RNA, ions and carbohydrates ... see detailed list of supported molecules), such as small-molecules, parameters and topology must be obtained and provided by the user, as there is currently no built-in solution to generate them on the fly.

More information about [topoaa] parameters can be accessed here or retrieved by running:

haddock3-cfg -m topoaa

Here an example configuration file snapshot of a typical execution of the [topoaa] module in which a user specifies the protonation state of the histidine residues:

# Definition of 
run_dir = "example"
molecules = [
 "DNA_structure.pdb",
 "1abc.pdb",
]

[topoaa]
autohis = false
# Specify molecule 1 specific parameters
[topoaa.mol1]
5_phosphate = true
# Specify molecule 2 specific parameters
[topoaa.mol2]
nhisd = 1
hisd_1 = 76
nhise = 1
hise_1 = 15
charged_nter = true
charged_cter = false

# Workflow continues with other modules
# ...

The [topoaa.mol1] in square brackets is not as module, but allows to specify topoaa parameters for a given molecule. In this case (mol1), the parameters will be applied to the first molecule in the list of input molecules ("1abc.pdb").

Notable parameters

  • autohis: If set to false, you will need to specify the protonation states of histidines manually.

Parameters specific to each molecule

  • [topoaa.molX]: Allows the definition of specific topoaa parameters for molecule X.
    • nhisd, nhise allow to define the number of HISD, HISE in the molecule.
    • hisd_Y, hise_Y, allow to define which residue needs to be modified (e.g: hisd_1 = 3 means that we are defining the first HISD residue, and this residue has residue index of 3 in the file).
    • charged_nter, charged_cter allow to define the state of Nter and Cter residues. Note that chain breaks are not evaluated as termini residues.
    • 5_phosphate: Allows to define the state of the 5' end of nucleic acids sequences. If set to true, 5' end will be a phosphate group. Otherwise it will be an OH. (default false). Note that chain breaks are not evaluated as 5' ends.