Tleap

Prepare Amber simulations with tleap.

FF_WATER_SOLVENT_BOX_MAP: dict[str, Any] = {'tip3p': 'TIP3PBOX', 'tip4p': 'TIP4PBOX', 'tip4pew': 'TIP4PEWBOX', 'tip5p': 'TIP5PBOX', 'opc': 'OPCBOX', 'opc3': 'OPC3BOX', 'pol3': 'POL3BOX', 'spce': 'SPCBOX'} module-attribute

Maps ff_water in simulation contexts to tleap box types.

TLEAP_PATH = os.environ.get('TLEAP_PATH', 'tleap') module-attribute

Path to tleap executable.

You can specify this by setting the path to the TLEAP_PATH environmental variable. For example:

export TLEAP_PATH="~/miniconda3/envs/metalflare-dev/bin/tleap

cli_run_tleap()

Command-line interface to running tleap

get_prelim_sim_info(pdb_path, simulation_context, add_lines=None)

Run a preliminary tleap preparation to get information about the system.

PARAMETER	DESCRIPTION
pdb_path	Path to PDB file to load into tleap. TYPE: str
simulation_context	A simulation context for system preparation. TYPE: SimulationContextManager
add_lines	Additional tleap lines to add before loading the PDB file. TYPE: Iterable[str] | None DEFAULT: None

RETURNS	DESCRIPTION
dict[str, Any]	Parsed information from the tleap log.

Examples:

The base tleap input file is shown below with AMBER_PROTEIN_STANDARD_CONTEXT.

source leaprc.protein.ff19SB
source leaprc.water.opc3
<add_lines>
mol = loadpdb <pdb_path>
solvatebox mol OPC3BOX 10.0
savepdb mol <temp file>
charge mol
quit

get_source_ff_lines(simulation_context)

Prepare tleap commands for loading force fields.

PARAMETER	DESCRIPTION
simulation_context	A simulation context for system preparation. TYPE: SimulationContextManager

RETURNS	DESCRIPTION
list[str]	source leaprc. commands for tleap.

Examples:

amber_context = {
    "ff_protein": "ff14SB", "ff_water": "tip3p", "ff_small_molecule": "gaff2"
}
simulation_context = SimulationContextManager(**amber_context)
tleap_lines = get_source_ff_lines(simulation_context)

would result in

["source leaprc.protein.ff14SB", "source leaprc.water.tip3p", "source leaprc.gaff2"]

parse_tleap_log(log_lines)

Parse information from tleap log file.

PARAMETER	DESCRIPTION
log_lines	Lines of the tleap.log file. TYPE: list[str]

RETURNS	DESCRIPTION
dict[str, Any]	Parsed information from the log file.

Information:

• duplicate_atoms: list[dict[str, str]]

  Each atom in a residue should have a unique type. This list collects information of duplicated atom types.

  [
      {'residue_number': 23, 'atom_type': 'ND2'},
      {'residue_number': 23, 'atom_type': 'OD1'},
      {'residue_number': 92, 'atom_type': 'NE2'}
  ]
  

prepare_amber_files(pdb_path, prmtop_path, inpcrd_path, simulation_context, pdb_output_path=None, cations=0, anions=0, add_lines=None)

Prepare amber input files.

PARAMETER	DESCRIPTION
pdb_path	Path to PDB file to load into tleap. TYPE: str
prmtop_path	Path to save topology file. TYPE: str
inpcrd	Path to save coordinate file.
simulation_context	A simulation context for system preparation. TYPE: SimulationContextManager
pdb_output_path	Path to save final system. TYPE: str | None DEFAULT: None
cations	Number of cations to add. TYPE: int DEFAULT: 0
anions	Number of anions to add. TYPE: int DEFAULT: 0
add_lines	Additional tleap lines to add before generating parameters. TYPE: Iterable[str] | None DEFAULT: None

RETURNS	DESCRIPTION
dict[str, Any]	Parsed information from the tleap log.

Examples:

The base tleap input file is shown below with AMBER_PROTEIN_STANDARD_CONTEXT.

source leaprc.protein.ff19SB
source leaprc.water.opc3
<add_lines>
mol = loadpdb <pdb_path>
addIons2 mol Na+ <cations>
addIons2 mol Cl- <anions>
solvatebox mol OPC3BOX 10.0
savepdb mol <temp file>
saveamberparm mol <prmtop_path> <inpcrd_path>
charge mol
quit

run_tleap(pdb_path, topo_path, coord_path, yaml_paths, work_dir=None)

Run tleap preparation of a system.

PARAMETER	DESCRIPTION
pdb_path	Path to PDB file to prepare. TYPE: str
topo_path	Path to save topology file. TYPE: str
coord_path	Path to save coordinate file. TYPE: str
yaml_paths	YAML file paths context. You can include a list under add_lines_tleap key for adding lines to the tleap preparation in get_prelim_sim_info. TYPE: Iterable[str]
work_dir	Working directory to run tleap and specifying relative paths. TYPE: str | None DEFAULT: None