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:
# ...
molecules = [
"1abc.pdb",
"2xyz.pdb"
]
[topoaa]
autohis = false
[topoaa.mol1]
nhisd = 0
nhise = 1
hise_1 = 75
[topoaa.mol2]
nhisd = 1
hisd_1 = 76
nhise = 1
hise_1 = 15
# Workflow continues
# ...