def get_parameters(cls, forcefield, water_model):
if forcefield == "charmm":
prms = [
"par_all36m_prot.prm", "par_all36_cgenff.prm",
"par_all36_lipid.prm", "par_all36_carb.prm",
"par_all36_na.prm", "toppar_all36_prot_na_combined.str"
]
if water_model == "tip3":
prms.append("toppar_water_ions.str")
elif water_model == "tip4e":
prms.append("toppar_water_ions_tip4p_ew.str")
elif water_model == "spce":
prms.append("toppar_water_ions_spc_e.str")
elif forcefield == "amber":
from dabble.param import AmberWriter # avoid circular dependency
return AmberWriter.get_parameters(forcefield, water_model)
elif forcefield == "opls":
prms = ["opls_aam.prm"]
if water_model != "tip3":
raise DabbleError("Only TIP3 water model supported for OPLS")
else:
raise ValueError("Invalid forcefield: '%s'" % forcefield)
return [cls._get_forcefield_path(par) for par in prms]
def get_parameters(cls, forcefield, water_model):
"""
Get the path to GROMACS-format parameter files for a given force field
"""
# Amber and Charmm handled by converstion
if forcefield == "charmm":
return CharmmWriter.get_parameters(forcefield, water_model)
if forcefield == "amber":
return AmberWriter.get_parameters(forcefield, water_model)
if forcefield == "opls":
return CharmmWriter.get_parameters(forcefield, water_model)
# Gromacs topologies and parameters are the same directories
return GromacsWriter.get_topologies(forcefield, water_model)