def readAmber12SB(main_file = None, mod_files = None):
global Amber12SB
if main_file is None and mod_files is None:
if Amber12SB is None:
paramfile = os.path.join(this_directory, "parm10.dat")
modfile = os.path.join(this_directory, "frcmod.ff12SB")
Amber12SB = AmberData.AmberParameters(paramfile,
[(modfile, 'MOD4')])
Amber12SB.lennard_jones_1_4 = 0.5
Amber12SB.electrostatic_1_4 = 1./1.2
Amber12SB.default_ljpar_set = Amber12SB.ljpar_sets['MOD4']
Amber12SB.atom_type_property = 'amber12_atom_type'
Amber12SB.charge_property = 'amber_charge'
return Amber12SB
else:
if main_file is None:
main_file = os.path.join(this_directory, "parm10.dat")
mod_files = [(fullModFilePath(mf), 'MOD4') for mf in mod_files]
mod_files.insert(0, (os.path.join(this_directory, "frcmod.ff12SB"),
'MOD4'))
params = AmberData.AmberParameters(main_file, mod_files)
params.lennard_jones_1_4 = 0.5
params.electrostatic_1_4 = 1./1.2
params.default_ljpar_set = params.ljpar_sets['MOD4']
params.atom_type_property = 'amber12_atom_type'
params.charge_property = 'amber_charge'
return params
def readAmber99(main_file=None, mod_files=None):
global Amber99
if main_file is None and mod_files is None:
if Amber99 is None:
paramfile = os.path.join(this_directory, "parm99.dat")
Amber99 = AmberData.AmberParameters(paramfile)
Amber99.lennard_jones_1_4 = 0.5
Amber99.electrostatic_1_4 = 1. / 1.2
Amber99.default_ljpar_set = Amber99.ljpar_sets['MOD4']
Amber99.atom_type_property = 'amber_atom_type'
Amber99.charge_property = 'amber_charge'
return Amber99
else:
if main_file is None:
main_file = os.path.join(this_directory, "parm99.dat")
if mod_files is None:
mod_files = []
else:
mod_files = map(lambda mf: (fullModFilePath(mf), 'MOD4'),
mod_files)
params = AmberData.AmberParameters(main_file, mod_files)
params.lennard_jones_1_4 = 0.5
params.electrostatic_1_4 = 1. / 1.2
params.default_ljpar_set = params.ljpar_sets['MOD4']
params.atom_type_property = 'amber_atom_type'
params.charge_property = 'amber_charge'
return params
def readOPLS(main_file=None, mod_files=None):
global OPLS
if main_file is None and mod_files is None:
if OPLS is None:
paramfile = os.path.join(this_directory, "opls_parm.dat")
OPLS = AmberData.AmberParameters(paramfile)
OPLS.lennard_jones_1_4 = 0.125
OPLS.electrostatic_1_4 = 0.5
OPLS.default_ljpar_set = OPLS.ljpar_sets['OPLS']
OPLS.atom_type_property = 'opls_atom_type'
OPLS.charge_property = 'opls_charge'
return OPLS
else:
if main_file is None:
main_file = os.path.join(this_directory, "opls_parm.dat")
if mod_files is None:
mod_files = []
else:
mod_files = map(lambda mf: (fullModFilePath(mf), 'OPLS'),
mod_files)
params = AmberData.AmberParameters(main_file, mod_files)
params.lennard_jones_1_4 = 0.125
params.electrostatic_1_4 = 0.5
params.default_ljpar_set = params.ljpar_sets['OPLS']
params.atom_type_property = 'opls_atom_type'
params.charge_property = 'opls_charge'
return params
def readAmber91():
global Amber91
if Amber91 is None:
Amber91 = AmberData.AmberParameters(os.path.join(this_directory,
"parm91.dat"))
Amber91.lennard_jones_1_4 = 0.5
Amber91.electrostatic_1_4 = 0.5
Amber91.default_ljpar_set = Amber91.ljpar_sets['STDA']
Amber91.atom_type_property = 'amber91_atom_type'
Amber91.charge_property = 'amber91_charge'
def readAmberFiles(main_file, std_mod_file, mod_files, atom_type_property,
charge_property, with_gaff):
main_file = os.path.join(this_directory, main_file)
if mod_files is None:
mod_files = []
else:
mod_files = [(fullModFilePath(mf), 'MOD4') for mf in mod_files]
if std_mod_file is not None:
mod_files.insert(0,
(os.path.join(this_directory, std_mod_file), 'MOD4'))
params = AmberData.AmberParameters(main_file, mod_files)
if with_gaff:
gaff_params = AmberData.AmberParameters(
os.path.join(this_directory, "gaff.dat"), [])
params.merge(gaff_params)
params.lennard_jones_1_4 = 0.5
params.electrostatic_1_4 = 1. / 1.2
params.default_ljpar_set = params.ljpar_sets['MOD4']
params.atom_type_property = atom_type_property
params.charge_property = charge_property
return params