def create_coords(self, curr_dir, dir_name, lig_morph, pdb_file, system,
cmd1, cmd2, boxdims):
"""
"""
mol2 = os.path.join(curr_dir, dir_name,
const.MORPH_NAME + const.MOL2_EXT)
util.write_mol2(lig_morph, mol2, False, self.zz_atoms)
# we should now have a new MOL2 with updated coordinates for the ligand
# these will have to be 'pasted' into the system and new crd/top be
# prepared
com = self.ff.Complex(pdb_file, mol2)
com.box_dims = boxdims
com.frcmod = self.frcmod
com.ligand_fmt = 'mol2'
com.prepare_top(gaff=self.gaff)
com.create_top(boxtype='set', addcmd=cmd1 + cmd2)
# FIXME: we do that already in setup but calling create_coords
# from morph.py has not picked up on this
lig_morph = finalise_morph(lig_morph, self.atoms_final, self.atom_map)
patch_element(com.amber_top, lig_morph, self.lig_initial,
self.lig_final, self.atom_map)
com.lig_flex()
if type(system) == self.ff.Complex:
com.prot_flex()
def setup(self, curr_dir, lig_morph, cmd1, cmd2):
patch_parms = []
if self.FE_sub_type[:8] == 'softcore':
state0, state1 = amber.softcore(lig_morph, self.lig_final,
self.atom_map)
pert0_info, pert1_info = None, None
elif self.FE_sub_type[:5] == 'dummy':
state0 = lig_morph
state1, pert0_info, pert1_info = \
amber.dummy(lig_morph, self.con_morph,
self.lig_final, self.atom_map)
else:
raise NotImplementedError
amber.write_mdin(self.atoms_initial, self.atoms_final, self.atom_map,
'pmemd', self.FE_sub_type, True)
mol2_0 = os.path.join(curr_dir,
const.MORPH_NAME + '0' + const.MOL2_EXT)
util.write_mol2(state0, mol2_0, resname=const.LIGAND0_NAME)
frcmod0 = os.path.join(curr_dir, const.MORPH_NAME + '0.frcmod')
mol2_1 = os.path.join(curr_dir,
const.MORPH_NAME + '1' + const.MOL2_EXT)
util.write_mol2(state1, mol2_1, resname=const.LIGAND1_NAME)
frcmod1 = os.path.join(curr_dir, const.MORPH_NAME + '1.frcmod')
lig = self.ff.Ligand(const.MORPH_NAME,
start_file=mol2_0,
start_fmt='mol2',
frcmod=frcmod0,
gaff=self.gaff)
lig.set_atomtype(self.gaff)
lig._parmchk(mol2_0, 'mol2', frcmod0)
lig._parmchk(mol2_1, 'mol2', frcmod1)
if self.FE_sub_type == 'softcore' or self.FE_sub_type == 'dummy':
lig._parm_overwrite = 'onestep'
self.files_created.extend(('onestep.parm7', 'onestep.rst7'))
if self.FE_sub_type == 'softcore3' or self.FE_sub_type == 'dummy3':
lig._parm_overwrite = 'vdw'
self.files_created.extend(('vdw.parm7', 'vdw.rst7'))
if self.FE_sub_type == 'softcore' or self.FE_sub_type == 'softcore3' \
or self.FE_sub_type == 'dummy3':
if pert0_info:
pert0 = pert0_info
else:
pert0 = ''
if pert1_info:
pert1 = pert1_info
else:
pert1 = ''
lig.prepare_top(pert=pert0)
lig.leap.add_mol(mol2_1, 'mol2', [frcmod1], pert=pert1)
lig.create_top(boxtype='', addcmd=cmd1 + cmd2)
if self.FE_sub_type == 'softcore2' or self.FE_sub_type == 'dummy2':
ow_add = '_int'
if self.FE_sub_type == 'dummy2':
f = True
else:
f = False
int_state = util.transfer_charges(state0, state1, self.atom_map, f)
mol2_int = os.path.join(curr_dir,
const.MORPH_NAME + ow_add + const.MOL2_EXT)
util.write_mol2(int_state, mol2_int, resname=const.INT_NAME)
lig = self.ff.Ligand(const.MORPH_NAME,
start_file=mol2_0,
start_fmt='mol2',
frcmod=frcmod0,
gaff=self.gaff)
lig.set_atomtype(self.gaff)
if self.dummies0:
lig._parm_overwrite = 'vdw'
patch_parms.append(
(lig._parm_overwrite, ':%s' % const.LIGAND0_NAME,
':%s' % const.INT_NAME))
else:
lig._parm_overwrite = 'charge'
lig.prepare_top(pert=pert0_info)
# intermediate state does never have dummies
lig.leap.add_mol(mol2_int, 'mol2', [frcmod1])
lig.create_top(boxtype='', addcmd=cmd1 + cmd2)
lig = self.ff.Ligand(const.MORPH_NAME,
start_file=mol2_int,
start_fmt='mol2',
frcmod=frcmod1,
gaff=self.gaff)
lig.set_atomtype(self.gaff)
if self.dummies1:
lig._parm_overwrite = 'vdw'
patch_parms.append(
(lig._parm_overwrite, ':%s' % const.INT_NAME,
':%s' % const.LIGAND1_NAME))
else:
lig._parm_overwrite = 'charge'
# intermediate state does never have dummies
lig.prepare_top()
lig.leap.add_mol(mol2_1, 'mol2', [frcmod0], pert=pert1_info)
lig.create_top(boxtype='', addcmd=cmd1 + cmd2)
self.files_created.extend(
('charge.parm7', 'charge.rst7', 'vdw.par7', 'vdw.rst7'))
# FIXME: residue name will be both the same
elif self.FE_sub_type == 'softcore3' or self.FE_sub_type == 'dummy3':
lig = self.ff.Ligand(const.MORPH_NAME,
start_file=mol2_0,
start_fmt='mol2',
frcmod=frcmod0,
gaff=self.gaff)
lig.set_atomtype(self.gaff)
lig._parm_overwrite = 'decharge'
patch_parms.append(
(lig._parm_overwrite, ':%s' % const.LIGAND0_NAME,
':%s' % const.LIGAND1_NAME))
lig.prepare_top(pert=pert0)
lig.leap.add_mol(mol2_0, 'mol2', [frcmod0], pert=pert0)
lig.create_top(boxtype='', addcmd=cmd1 + cmd2)
lig = self.ff.Ligand(const.MORPH_NAME,
start_file=mol2_1,
start_fmt='mol2',
frcmod=frcmod1,
gaff=self.gaff)
lig.set_atomtype(self.gaff)
lig._parm_overwrite = 'recharge'
if pert1_info:
pert = pert1_info
else:
pert = ''
lig.prepare_top(pert=pert1)
lig.leap.add_mol(mol2_1, 'mol2', [frcmod1], pert=pert1)
lig.create_top(boxtype='', addcmd=cmd1 + cmd2)
self.files_created.extend(('recharge.parm7', 'recharge.rst7',
'decharge.parm7', 'decharge.rst7'))
elif self.FE_sub_type == 'dummy':
lig.prepare_top(pert=pert0_info)
lig.leap.add_mol(mol2_1, 'mol2', [frcmod1], pert=pert1_info)
lig.create_top(boxtype='', addcmd=cmd1 + cmd2)
self.frcmod0 = frcmod0
self.frcmod1 = frcmod1
if self.FE_sub_type[:5] == 'dummy':
for prm in patch_parms:
util.patch_parmtop(prm[0] + lig.TOP_EXT, "", prm[1], prm[2])
def create_coords(self, curr_dir, dir_name, lig_morph, pdb_file, system,
cmd1, cmd2, boxdims):
patch_parms = []
if self.FE_sub_type[:8] == 'softcore':
state0, state1 = \
amber.softcore(lig_morph, self.lig_final,
self.atom_map)
pert0_info, pert1_info = None, None
elif self.FE_sub_type[:5] == 'dummy':
state0 = lig_morph
state1, pert0_info, pert1_info = \
amber.dummy(lig_morph, self.con_morph,
self.lig_final, self.atom_map)
else:
raise NotImplementedError
amber.write_mdin(self.atoms_initial, self.atoms_final, self.atom_map,
'pmemd', self.FE_sub_type, False)
mol2_0 = os.path.join(curr_dir,
const.MORPH_NAME + '0' + const.MOL2_EXT)
util.write_mol2(state0, mol2_0, resname=const.LIGAND0_NAME)
mol2_1 = os.path.join(curr_dir,
const.MORPH_NAME + '1' + const.MOL2_EXT)
util.write_mol2(state1, mol2_1, resname=const.LIGAND1_NAME)
com = self.ff.Complex(pdb_file, mol2_0)
com.__class__.SSBONDS_OFFSET = 2 # FIXME: kludge
com.box_dims = boxdims
com.ligand_fmt = 'mol2'
com.frcmod = self.frcmod0
if self.FE_sub_type == 'softcore' or self.FE_sub_type == 'dummy':
com._parm_overwrite = 'onestep'
if self.FE_sub_type == 'softcore3' or self.FE_sub_type == 'dummy3':
com._parm_overwrite = 'vdw'
if self.FE_sub_type == 'softcore' or self.FE_sub_type == 'softcore3' \
or self.FE_sub_type == 'dummy3':
if pert0_info:
pert0 = pert0_info
else:
pert0 = ''
if pert1_info:
pert1 = pert1_info
else:
pert1 = ''
com.prepare_top(gaff=self.gaff, pert=pert0)
com.leap.add_mol(mol2_1, 'mol2', [self.frcmod1], pert=pert1)
com.create_top(boxtype='set', addcmd=cmd1 + cmd2)
if self.FE_sub_type == 'softcore2' or self.FE_sub_type == 'dummy2':
ow_add = '_int'
if self.FE_sub_type == 'dummy2':
f = True
else:
f = False
int_state = util.transfer_charges(state0, state1, self.atom_map, f)
mol2_int = os.path.join(curr_dir,
const.MORPH_NAME + ow_add + const.MOL2_EXT)
util.write_mol2(int_state, mol2_int, resname=const.INT_NAME)
com = self.ff.Complex(pdb_file, mol2_0)
com.__class__.SSBONDS_OFFSET = 2 # FIXME: kludge
com.box_dims = boxdims
com.ligand_fmt = 'mol2'
com.frcmod = self.frcmod0
if self.dummies0:
com._parm_overwrite = 'vdw'
patch_parms.append(
(com._parm_overwrite, ':%s' % const.LIGAND0_NAME,
':%s' % const.INT_NAME))
else:
com._parm_overwrite = 'charge'
com.prepare_top(gaff=self.gaff, pert=pert0_info)
# intermediate state does never have dummies
com.leap.add_mol(mol2_int, 'mol2', [self.frcmod1])
com.create_top(boxtype='set', addcmd=cmd1 + cmd2)
com = self.ff.Complex(pdb_file, mol2_int)
com.__class__.SSBONDS_OFFSET = 2 # FIXME: kludge
com.box_dims = boxdims
com.ligand_fmt = 'mol2'
com.frcmod = self.frcmod1
if self.dummies1:
com._parm_overwrite = 'vdw'
patch_parms.append(
(com._parm_overwrite, ':%s' % const.INT_NAME,
':%s' % const.LIGAND1_NAME))
else:
com._parm_overwrite = 'charge'
# intermediate state does never have dummies
com.prepare_top(gaff=self.gaff)
com.leap.add_mol(mol2_1, 'mol2', [self.frcmod0], pert=pert1_info)
com.create_top(boxtype='set', addcmd=cmd1 + cmd2)
# FIXME: residue name will be both the same
elif self.FE_sub_type == 'softcore3' or self.FE_sub_type == 'dummy3':
com = self.ff.Complex(pdb_file, mol2_0)
com.__class__.SSBONDS_OFFSET = 2 # FIXME: kludge
com.box_dims = boxdims
com.ligand_fmt = 'mol2'
com.frcmod = self.frcmod0
com._parm_overwrite = 'decharge'
com.prepare_top(gaff=self.gaff, pert=pert0)
com.leap.add_mol(mol2_0, 'mol2', [self.frcmod0], pert=pert0)
com.create_top(boxtype='set', addcmd=cmd1 + cmd2)
com = self.ff.Complex(pdb_file, mol2_1)
com.__class__.SSBONDS_OFFSET = 2 # FIXME: kludge
com.box_dims = boxdims
com.ligand_fmt = 'mol2'
com.frcmod = self.frcmod1
com._parm_overwrite = 'recharge'
com.prepare_top(gaff=self.gaff, pert=pert1)
com.leap.add_mol(mol2_1, 'mol2', [self.frcmod1], pert=pert1)
com.create_top(boxtype='set', addcmd=cmd1 + cmd2)
elif self.FE_sub_type == 'dummy':
com.prepare_top(gaff=self.gaff, pert=pert0_info)
com.leap.add_mol(mol2_1, 'mol2', [self.frcmod1], pert=pert1_info)
com.create_top(boxtype='set', addcmd=cmd1 + cmd2)
if self.FE_sub_type[:5] == 'dummy':
for prm in patch_parms:
util.patch_parmtop(prm[0] + com.TOP_EXT, "", prm[1], prm[2])
def setup(self, curr_dir, lig_morph, cmd1, cmd2):
if self.FE_sub_type[:8] == 'softcore':
state0, state1 = \
amber.softcore(lig_morph, self.lig_final,
self.atom_map)
pert0_info, pert1_info = None, None
elif self.FE_sub_type[:5] == 'dummy':
# also for Gromacs and CHARMM
state0 = lig_morph
state1, pert0_info, pert1_info = \
amber.dummy(lig_morph, self.con_morph,
self.lig_final, self.atom_map)
else:
raise NotImplementedError
if self.mdin:
amber.write_mdin(self.atoms_initial, self.atoms_final,
self.atom_map, 'sander', self.FE_sub_type, True)
mol2_0 = os.path.join(curr_dir,
const.MORPH_NAME + '0' + const.MOL2_EXT)
util.write_mol2(state0, mol2_0)
frcmod0 = os.path.join(curr_dir, const.MORPH_NAME + '0.frcmod')
lig0 = self.ff.Ligand(const.MORPH_NAME,
start_file=mol2_0,
start_fmt='mol2',
frcmod=frcmod0,
gaff=self.gaff)
lig0.set_atomtype(self.gaff)
lig0._parmchk(mol2_0, 'mol2', frcmod0)
lig0._parm_overwrite = 'state0'
if pert0_info:
lig0.prepare_top(pert=pert0_info)
else:
lig0.prepare_top()
lig0.create_top(boxtype='', addcmd=cmd1 + cmd2)
mol2_1 = os.path.join(curr_dir,
const.MORPH_NAME + '1' + const.MOL2_EXT)
util.write_mol2(state1, mol2_1)
frcmod1 = os.path.join(curr_dir, const.MORPH_NAME + '1.frcmod')
lig1 = self.ff.Ligand(const.MORPH_NAME,
start_file=mol2_1,
start_fmt='mol2',
frcmod=frcmod1,
gaff=self.gaff)
lig1.set_atomtype(self.gaff)
lig1._parmchk(mol2_1, 'mol2', frcmod1)
lig1._parm_overwrite = 'state1'
if pert1_info:
lig1.prepare_top(pert=pert1_info)
else:
lig1.prepare_top()
lig1.create_top(boxtype='', addcmd=cmd1 + cmd2)
self.lig0 = lig0
self.lig1 = lig1
self.frcmod0 = frcmod0
self.frcmod1 = frcmod1
# NOTE: intermediate state assumed to not have dummies, so no
# missing parameters fixed through patching!
if self.FE_sub_type == 'softcore2' or self.FE_sub_type == 'dummy2':
ow_add = '_int'
if self.FE_sub_type == 'dummy2':
f = True
else:
f = False
int_state = util.transfer_charges(state0, state1, self.atom_map, f)
mol2_int = os.path.join(curr_dir,
const.MORPH_NAME + ow_add + const.MOL2_EXT)
util.write_mol2(int_state, mol2_int, resname=const.INT_NAME)
lig = self.ff.Ligand(const.MORPH_NAME,
start_file=mol2_int,
start_fmt='mol2',
frcmod=frcmod0,
gaff=self.gaff)
lig.set_atomtype(self.gaff)
lig._parm_overwrite = 'state_int'
lig.prepare_top(add_frcmods=[frcmod1])
lig.create_top(boxtype='', addcmd=cmd1 + cmd2)
if self.FE_sub_type == 'dummy' or self.FE_sub_type == 'dummy2':
top0 = lig0._parm_overwrite + lig0.TOP_EXT
top1 = lig1._parm_overwrite + lig1.TOP_EXT
util.patch_parmtop(top0, top1, ':%s' % const.LIGAND_NAME, '')
if self.FE_sub_type == 'dummy3':
ow_add = '_int'
int_mol = util.zero_charges(state1, self.atom_map)
mol2_int = os.path.join(curr_dir,
const.MORPH_NAME + ow_add + const.MOL2_EXT)
util.write_mol2(int_mol, mol2_int, resname=const.LIGAND_NAME)
lig = self.ff.Ligand(const.MORPH_NAME,
start_file=mol2_int,
start_fmt='mol2',
frcmod=frcmod1,
gaff=self.gaff)
lig.set_atomtype(self.gaff)
lig._parm_overwrite = 'state_int'
lig.prepare_top(pert=pert1_info)
lig.create_top(boxtype='')
top0 = lig0._parm_overwrite + lig0.TOP_EXT
int_name = lig._parm_overwrite + lig.TOP_EXT
top1 = lig1._parm_overwrite + lig1.TOP_EXT
util.patch_parmtop(top0, int_name, ':%s' % const.LIGAND_NAME, '')
util.patch_parmtop(int_name, top1, ':%s' % const.LIGAND_NAME, '')
self.int_state = lig
def create_coords(self, curr_dir, dir_name, lig_morph, pdb_file, system,
cmd1, cmd2, boxdims):
if self.FE_sub_type[:8] == 'softcore':
state0, state1 = \
amber.softcore(lig_morph, self.lig_final,
self.atom_map)
pert0_info, pert1_info = None, None
elif self.FE_sub_type[:5] == 'dummy':
# also for Gromacs and CHARMM
state0 = lig_morph
state1, pert0_info, pert1_info = \
amber.dummy(lig_morph, self.con_morph,
self.lig_final, self.atom_map)
leap_extra = 'source "%s"\n'
else:
raise NotImplementedError
if self.mdin:
amber.write_mdin(self.atoms_initial, self.atoms_final,
self.atom_map, 'sander', self.FE_sub_type, False)
mol2_0 = os.path.join(curr_dir,
const.MORPH_NAME + '0' + const.MOL2_EXT)
util.write_mol2(state0, mol2_0)
com0 = self.ff.Complex(pdb_file, mol2_0)
com0.box_dims = boxdims
com0.ligand_fmt = 'mol2'
com0.frcmod = self.frcmod0
com0._parm_overwrite = 'state0'
com0.ligand_fmt = 'mol2'
if pert0_info:
com0.prepare_top(gaff=self.gaff, pert=pert0_info)
else:
com0.prepare_top(gaff=self.gaff)
com0.create_top(boxtype='set', addcmd=cmd1 + cmd2)
mol2_1 = os.path.join(curr_dir,
const.MORPH_NAME + '1' + const.MOL2_EXT)
util.write_mol2(state1, mol2_1)
com1 = self.ff.Complex(pdb_file, mol2_1)
com1.box_dims = boxdims
com1.ligand_fmt = 'mol2'
com1.frcmod = self.frcmod1
com1._parm_overwrite = 'state1'
if pert1_info:
com1.prepare_top(gaff=self.gaff, pert=pert1_info)
else:
com1.prepare_top(gaff=self.gaff)
com1.create_top(boxtype='set', addcmd=cmd1 + cmd2)
if self.FE_sub_type == 'softcore2' or self.FE_sub_type == 'dummy2':
ow_add = '_int'
if self.FE_sub_type == 'dummy2':
f = True
else:
f = False
int_state = util.transfer_charges(state0, state1, self.atom_map, f)
mol2_int = os.path.join(curr_dir,
const.MORPH_NAME + ow_add + const.MOL2_EXT)
util.write_mol2(int_state, mol2_int, resname=const.INT_NAME)
com = self.ff.Complex(pdb_file, mol2_int)
com.box_dims = boxdims
com.ligand_fmt = 'mol2'
com.frcmod = self.frcmod1
com._parm_overwrite = 'state_int'
com.prepare_top(add_frcmods=[self.frcmod0])
com.create_top(boxtype='set', addcmd=cmd1 + cmd2)
if self.FE_sub_type == 'dummy' or self.FE_sub_type == 'dummy2':
top0 = com0._parm_overwrite + com0.TOP_EXT
top1 = com1._parm_overwrite + com1.TOP_EXT
util.patch_parmtop(top0, top1, ':%s' % const.LIGAND_NAME, '')
self.parmtop = top0
self.inpcrd = com0._parm_overwrite + com0.RST_EXT
if self.FE_sub_type == 'dummy3': # for GROMACS and CHARMM
ow_add = '_int'
int_mol = util.zero_charges(state1, self.atom_map)
mol2_int = os.path.join(curr_dir,
const.MORPH_NAME + ow_add + const.MOL2_EXT)
util.write_mol2(int_mol, mol2_int, resname=const.LIGAND_NAME)
com = self.ff.Complex(pdb_file, mol2_int)
com.box_dims = boxdims
com.ligand_fmt = 'mol2'
com.frcmod = self.frcmod1
com._parm_overwrite = 'state_int'
if pert1_info:
com.prepare_top(gaff=self.gaff, pert=pert1_info)
else:
com.prepare_top(gaff=self.gaff)
com.create_top(boxtype='set')
top0 = com0._parm_overwrite + com0.TOP_EXT
int_name = com._parm_overwrite + com.TOP_EXT
top1 = com1._parm_overwrite + com1.TOP_EXT
util.patch_parmtop(top0, int_name, ':%s' % const.LIGAND_NAME, '')
util.patch_parmtop(int_name, top1, ':%s' % const.LIGAND_NAME, '')
self.parmtop0 = top0
self.inpcrd0 = com0._parm_overwrite + com0.RST_EXT
self.parmtop1 = top1
self.inpcrd1 = com1._parm_overwrite + com1.RST_EXT
self.int_state = com
def setup(self, curr_dir, lig_morph, cmd1, cmd2):
"""
"""
mol2 = os.path.join(curr_dir, const.MORPH_NAME + const.MOL2_EXT)
util.write_mol2(lig_morph, mol2, False, self.zz_atoms)
# create a new Ligand from the MOL2
self.frcmod = os.path.join(curr_dir, const.MORPH_NAME + '.frcmod')
# FIXME: Ligand class needs some redesign!
lig = self.ff.Ligand(const.MORPH_NAME,
start_file=mol2,
start_fmt='mol2',
frcmod=self.frcmod,
gaff=self.gaff)
# prevent antechamber from running over the MOL2 file
lig.set_atomtype(self.gaff)
lig._parmchk(mol2, 'mol2', self.frcmod)
lig.prepare_top()
lig.create_top(boxtype='', addcmd=cmd1 + cmd2)
lig.flex()
# To get the bonded parameters we reload the morph topolgy because
# lig_morph does not have the "amberparameters" property. Would it be
# possible to create those? We assume the ligand is the first molecule.
top, crd = lig.amber_top, lig.amber_crd
try:
molecules = Sire.IO.Amber().readCrdTop(crd, top)[0]
except UserWarning as error:
raise errors.SetupError('error opening %s/%s: %s' %
(crd, top, error))
new_morph = molecules.first().molecule()
lig_morph = finalise_morph(lig_morph, self.atoms_final, self.atom_map)
# FIXME: adapt for step protocols
if self.FE_sub_type == 'dummy':
make_pert_file(lig_morph, new_morph, 'onestep', 'initial_charge',
'final_charge', 'initial_LJ', 'final_LJ',
'initial_ambertype', 'final_ambertype',
self.lig_initial, self.lig_final, self.atoms_final,
self.atom_map, self.reverse_atom_map, self.zz_atoms,
False)
self.files_created.extend(
('onestep.parm7', 'onestep.rst7', const.MORPH_NAME +
os.extsep + 'onestep' + os.extsep + 'pert'))
elif self.FE_sub_type == 'dummy2':
if self.dummies0:
make_pert_file(lig_morph, new_morph, 'charge',
'initial_charge', 'final_charge', 'final_LJ',
'final_LJ', 'final_ambertype',
'final_ambertype', self.lig_initial,
self.lig_final, self.atoms_final, self.atom_map,
self.reverse_atom_map, self.zz_atoms, True)
make_pert_file(lig_morph, new_morph, 'vdw', 'initial_charge',
'initial_charge', 'initial_LJ', 'final_LJ',
'initial_ambertype', 'final_ambertype',
self.lig_initial, self.lig_final,
self.atoms_final, self.atom_map,
self.reverse_atom_map, self.zz_atoms, False)
else:
make_pert_file(lig_morph, new_morph, 'charge',
'initial_charge', 'final_charge', 'initial_LJ',
'initial_LJ', 'initial_ambertype',
'initial_ambertype', self.lig_initial,
self.lig_final, self.atoms_final, self.atom_map,
self.reverse_atom_map, self.zz_atoms, True)
make_pert_file(lig_morph, new_morph, 'vdw', 'final_charge',
'final_charge', 'initial_LJ', 'final_LJ',
'initial_ambertype', 'final_ambertype',
self.lig_initial, self.lig_final,
self.atoms_final, self.atom_map,
self.reverse_atom_map, self.zz_atoms, False)
self.files_created.extend(
('charge.parm7', 'charge.rst7',
const.MORPH_NAME + os.extsep + 'charge' + os.extsep + 'pert',
'vdw.parm7', 'vdw.rst7',
const.MORPH_NAME + os.extsep + 'vdw' + os.extsep + 'pert'))
elif self.FE_sub_type == 'dummy3':
make_pert_file(lig_morph, new_morph, 'decharge', 'initial_charge',
'zero_all', 'initial_LJ', 'initial_LJ',
'initial_ambertype', 'initial_ambertype',
self.lig_initial, self.lig_final, self.atoms_final,
self.atom_map, self.reverse_atom_map, self.zz_atoms,
False)
make_pert_file(lig_morph, new_morph, 'vdw', 'zero_all', 'zero_all',
'initial_LJ', 'final_LJ', 'initial_ambertype',
'final_ambertype', self.lig_initial, self.lig_final,
self.atoms_final, self.atom_map,
self.reverse_atom_map, self.zz_atoms, False)
make_pert_file(lig_morph, new_morph, 'recharge', 'zero_all',
'final_charge', 'final_LJ', 'final_LJ',
'final_ambertype', 'final_ambertype',
self.lig_initial, self.lig_final, self.atoms_final,
self.atom_map, self.reverse_atom_map, self.zz_atoms,
False)
self.files_created.extend(
('decharge.parm7', 'decharge.rst7', const.MORPH_NAME +
os.extsep + 'decharge' + os.extsep + 'pert', 'vdw.parm7',
'vdw.rst7', const.MORPH_NAME + os.extsep + 'vdw' + os.extsep +
'pert', 'recharge.parm7', 'recharge.rst7', const.MORPH_NAME +
os.extsep + 'recharge' + os.extsep + 'pert'))
patch_element(lig.amber_top, lig_morph, self.lig_initial,
self.lig_final, self.atom_map)