pygromos.files.forcefield.amber package

Submodules

pygromos.files.forcefield.amber.amberff module

class pygromos.files.forcefield.amber.amberff.AmberFF(name: str = 'amber', path_to_files: Optional[str] = None, auto_import: bool = True, verbose: bool = False)[source]

Bases: pygromos.files.forcefield._generic_force_field._generic_force_field

auto_import_ff()[source]
clean = False
create_cnf(mol: str, in_cnf: Optional[pygromos.files.topology.top.Top] = None, work_folder: Optional[str] = None, in_mol2_file: Optional[str] = None, gromosPP: Optional[pygromos.gromos.gromosPP.GromosPP] = None) → pygromos.files.coord.cnf.Cnf[source]
create_mol2(mol: Optional[str] = None)[source]
create_top(mol: str, in_top: pygromos.files.topology.top.Top, in_mol2_file: Optional[str] = None, work_folder: Optional[str] = None, gromosPP: Optional[pygromos.gromos.gromosPP.GromosPP] = None) → pygromos.files.topology.top.Top[source]
solvate = False
solventbox = 'TIP3PBOX'
class pygromos.files.forcefield.amber.amberff.amber2gromos(in_mol2_file: str, mol: rdkit.Chem.rdchem.Mol, gromosPP: pygromos.gromos.gromosPP.GromosPP, forcefield: pygromos.files.forcefield._generic_force_field._generic_force_field, work_folder: str = '.', solvate: bool = False, solventbox: Optional[str] = None, clean: bool = False)[source]

Bases: object

__init__(in_mol2_file: str, mol: rdkit.Chem.rdchem.Mol, gromosPP: pygromos.gromos.gromosPP.GromosPP, forcefield: pygromos.files.forcefield._generic_force_field._generic_force_field, work_folder: str = '.', solvate: bool = False, solventbox: Optional[str] = None, clean: bool = False)[source]

uses the ambertools programs antechamber, parmchk, and tleap together with the GROMOS++ program amber2gromos to generate a GROMOS topology and coordinate file for a given molecule

Parameters

  • in_mol2_file (str) – mol2 file for molecule to be parameterized

  • mol (Chem.rdchem.Mol) – rdkit molecule of the molecule in in_mol2_file

  • gromosPP (GromosPP)

  • forcefield (forcefield_system)

  • work_folder (str, optional) – where to generate the topology + cnf (default: “.”)

  • solvate (bool, optional) – should the topology be solvated? (default: False)

  • solventbox (str, optional) – what solvent should be used for solvation? e.g. TIP3PBOX or CHCL3BOX (default: TIP3PBOX)

  • clean (bool, optional) – should temporary ambertool files be removed after parameterization? (default: False)

amber2gromos()[source]

converts an AMBER (GAFF) parameter and crd file to a GROMOS top and cnf file

antechamber()[source]

executes the ambertools program antechamber

cleanup()[source]

removes temporary parmchk, antechamber, and tleap directories

get_gromos_coordinate_file()[source]
Returns

returns the path to the converted GROMOS coordinate file

Return type

str

get_gromos_topology() → str[source]
Returns

returns the path to the converted GROMOS topology

Return type

str

parmchk()[source]

executes the ambertools program parmchk

tleap()[source]

executes the ambertools program tleap

Module contents