Topo
FF_WATER_SOLVENT_BOX_MAP = {'tip3p': 'TIP3PBOX', 'tip4p': 'TIP4PBOX', 'tip4pew': 'TIP4PEWBOX', 'tip5p': 'TIP5PBOX', 'opc': 'OPCBOX', 'opc3': 'OPC3BOX', 'pol3': 'POL3BOX', 'spce': 'SPCBOX'}
¶
Maps ff_water
in simulation contexts to tleap box types.
TLEAP_PATH = os.environ.get('TLEAP_PATH', 'tleap')
¶
AmberTopoGen()
¶
Bases: TopoGen
Standardized framework for generating topology files.
dry_run(path_structure, simlify_config)
¶
Perform a dry run to obtain any preliminary information.
PARAMETER | DESCRIPTION |
---|---|
path_structure
|
Path structure file for topology generation. For Amber, this must be a PDB file.
TYPE:
|
simlify_config
|
Simlify configuration.
TYPE:
|
RETURNS | DESCRIPTION |
---|---|
dict[str, Any]
|
Keyword arguments to be passed into |
Examples:
The base tleap
input file is shown below with
[AMBER_PROTEIN_STANDARD_CONTEXT
][simulation.amber.contexts.AMBER_PROTEIN_STANDARD_CONTEXT].
ff_lines(simlify_config)
¶
Prepare to use force fields in the topology file.
PARAMETER | DESCRIPTION |
---|---|
simlify_config
|
A simulation context for system preparation.
TYPE:
|
RETURNS | DESCRIPTION |
---|---|
Iterable[str]
|
|
Examples:
amber_context = {
"ff_protein": "ff14SB", "ff_water": "tip3p", "ff_small_molecule": "gaff2"
}
simlify_config = SimulationContextManager(**amber_context)
tleap_lines = get_source_ff_lines(simlify_config)
would result in
run(path_structure, simlify_config, **kwargs)
¶
Run tleap preparation of a system.
PARAMETER | DESCRIPTION |
---|---|
path_structure
|
Path structure file for topology generation. For Amber, this must be a PDB file.
TYPE:
|
path_topo_write
|
Where to write topology file.
|
path_coord_write
|
Where to write coordinate file.
|
simlify_config
|
Simlify configuration.
TYPE:
|
dir_work
|
Working directory to generate topology. Useful for specifying relative paths.
|
kwargs
|
Keyword arguments used for this specific package. Required
Optional
|