def get_topologies(cls, forcefield, water_model):
if forcefield == "charmm":
topos = [
"top_all36_caps.rtf", "top_all36_cgenff.rtf",
"top_all36_prot.rtf", "top_all36_lipid.rtf",
"top_all36_carb.rtf", "top_all36_na.rtf",
"toppar_all36_prot_na_combined.str",
"toppar_all36_prot_fluoro_alkanes.str"
]
if water_model == "tip3":
topos.append("toppar_water_ions.str")
elif water_model == "tip4e":
topos.append("toppar_water_ions_tip4p_ew.str")
elif water_model == "spce":
topos.append("toppar_water_ions_spc_e.str")
elif forcefield == "opls":
topos = ["opls_aam.rtf", "opls_aam_caps.rtf"]
if water_model != "tip3":
raise DabbleError("Only TIP3 water model supported for OPLS")
elif forcefield == "amber":
from dabble.param import AmberWriter # avoid circular dependency
return AmberWriter.get_topologies(forcefield, water_model)
else:
raise ValueError("Invalid forcefield: '%s'" % forcefield)
return [cls._get_forcefield_path(top) for top in topos]
def get_topologies(cls, forcefield, water_model):
"""
Gets the path to GROMACS-format topologies for a given force field
"""
# Amber, Charmm, and OPLS handled by conversion
if forcefield == "charmm":
return CharmmWriter.get_topologies(forcefield, water_model)
if forcefield == "amber":
return AmberWriter.get_topologies(forcefield, water_model)
if forcefield == "opls":
return CharmmWriter.get_topologies(forcefield, water_model)
# No forcefields really ship with gromacs right now because
# I found an error in the OPLS AA/M gromacs implementation and
# they won't respond to my emails
# Use GROMACS forcefield for the remaining ones
#if forcefield == "opls":
# ffdir = "oplsaam.ff"
#elif forcefield == "gromos":
# ffdir = "gromos54a7.ff"
raise DabbleError("Unsupported forcefield %s" % forcefield)