def test_amber_binary_mixture():
sustiva_filename = utils.get_data_filename("chemicals/etoh/etoh.mol2")
etoh_filename = utils.get_data_filename("chemicals/etoh/etoh_renamed.mol2")
trj0, trj1 = md.load(sustiva_filename), md.load(etoh_filename)
# Hack to assign unique residue names that are consistent with contents of mol2 files
trj0.top.residue(0).name = "LIG"
trj1.top.residue(0).name = "LI2"
trj_list = [trj0, trj1]
with utils.enter_temp_directory(
): # Prevents creating tons of GAFF files everywhere.
box_filename = "./box.pdb"
box_trj = packmol.pack_box(trj_list, [25, 50])
box_trj.save(box_filename)
gaff_mol2_filename0, frcmod_filename0 = amber.run_antechamber(
"sustiva", sustiva_filename, charge_method=None)
gaff_mol2_filename1, frcmod_filename1 = amber.run_antechamber(
"etoh", etoh_filename, charge_method=None)
mol2_filenames = [gaff_mol2_filename0, gaff_mol2_filename1]
frcmod_filenames = [frcmod_filename0, frcmod_filename1]
prmtop_filename = "./out.prmtop"
inpcrd_filename = "./out.inpcrd"
tleap_cmd = amber.build_mixture_prmtop(mol2_filenames,
frcmod_filenames, box_filename,
prmtop_filename,
inpcrd_filename)
print(tleap_cmd)
def test_amber_box():
etoh_filename = utils.get_data_filename("chemicals/etoh/etoh.mol2")
trj_list = [md.load(etoh_filename)]
with utils.enter_temp_directory(
): # Prevents creating tons of GAFF files everywhere.
box_filename = "./box.pdb"
box_trj = packmol.pack_box(trj_list, [50])
box_trj.save(box_filename)
gaff_mol2_filename1, frcmod_filename1 = amber.run_antechamber(
"etoh", etoh_filename, charge_method=None)
mol2_filenames = [gaff_mol2_filename1]
frcmod_filenames = [frcmod_filename1]
prmtop_filename = "./out.prmtop"
inpcrd_filename = "./out.inpcrd"
tleap_cmd = amber.build_mixture_prmtop(mol2_filenames,
frcmod_filenames, box_filename,
prmtop_filename,
inpcrd_filename)
print(tleap_cmd)
def test_amber_binary_mixture():
sustiva_filename = utils.get_data_filename("chemicals/etoh/etoh.mol2")
etoh_filename = utils.get_data_filename("chemicals/etoh/etoh_renamed.mol2")
trj0, trj1 = md.load(sustiva_filename), md.load(etoh_filename)
# Hack to assign unique residue names that are consistent with contents of mol2 files
trj0.top.residue(0).name = "LIG"
trj1.top.residue(0).name = "LI2"
trj_list = [trj0, trj1]
with utils.enter_temp_directory(): # Prevents creating tons of GAFF files everywhere.
box_filename = "./box.pdb"
box_trj = packmol.pack_box(trj_list, [25, 50])
box_trj.save(box_filename)
gaff_mol2_filename0, frcmod_filename0 = amber.run_antechamber("sustiva", sustiva_filename, charge_method=None)
gaff_mol2_filename1, frcmod_filename1 = amber.run_antechamber("etoh", etoh_filename, charge_method=None)
mol2_filenames = [gaff_mol2_filename0, gaff_mol2_filename1]
frcmod_filenames = [frcmod_filename0, frcmod_filename1]
prmtop_filename = "./out.prmtop"
inpcrd_filename = "./out.inpcrd"
tleap_cmd = amber.build_mixture_prmtop(mol2_filenames, frcmod_filenames, box_filename, prmtop_filename, inpcrd_filename)
print(tleap_cmd)
def test_amber_water_mixture():
water_filename = utils.get_data_filename("chemicals/water/water.mol2")
etoh_filename = utils.get_data_filename("chemicals/etoh/etoh.mol2")
sustiva_filename = utils.get_data_filename("chemicals/sustiva/sustiva.mol2")
with utils.enter_temp_directory(): # Prevents creating tons of GAFF files everywhere.
shutil.copy( water_filename, 'c1.mol2' )
shutil.copy( etoh_filename, 'c2.mol2' )
shutil.copy( sustiva_filename, 'c3.mol2')
water_filename = 'c1.mol2'
etoh_filename = 'c2.mol2'
sustiva_filename = 'c3.mol2'
#Randomize residue names to avoid clashes
utils.randomize_mol2_residue_names( [ water_filename, etoh_filename, sustiva_filename] )
trj0, trj1, trj2 = md.load(water_filename), md.load(etoh_filename), md.load(sustiva_filename)
trj_list = [trj0, trj1, trj2]
box_filename = "./box.pdb"
box_trj = packmol.pack_box(trj_list, [300, 25, 3])
box_trj.save(box_filename)
gaff_mol2_filename0, frcmod_filename0 = amber.run_antechamber("water", water_filename, charge_method=None)
gaff_mol2_filename1, frcmod_filename1 = amber.run_antechamber("etoh", etoh_filename, charge_method=None)
gaff_mol2_filename2, frcmod_filename2 = amber.run_antechamber("sustiva", sustiva_filename, charge_method=None)
mol2_filenames = [gaff_mol2_filename0, gaff_mol2_filename1, gaff_mol2_filename2]
frcmod_filenames = [frcmod_filename0, frcmod_filename1, frcmod_filename2]
prmtop_filename = "./out.prmtop"
inpcrd_filename = "./out.inpcrd"
shutil.copy(box_filename, 'renamed.pdb')
tleap_cmd = amber.build_mixture_prmtop(mol2_filenames, frcmod_filenames, 'renamed.pdb', prmtop_filename, inpcrd_filename)
print(tleap_cmd)
#Also do here for case of GAFF water
tleap_cmd = amber.build_mixture_prmtop(mol2_filenames, frcmod_filenames, box_filename, prmtop_filename, inpcrd_filename, water_model = None)
print(tleap_cmd)
#Also do here for case of SPC
tleap_cmd = amber.build_mixture_prmtop(mol2_filenames, frcmod_filenames, 'renamed.pdb', prmtop_filename, inpcrd_filename, water_model = 'SPC')
print(tleap_cmd)
def test_amber_box():
etoh_filename = utils.get_data_filename("chemicals/etoh/etoh.mol2")
trj_list = [md.load(etoh_filename)]
with utils.enter_temp_directory(): # Prevents creating tons of GAFF files everywhere.
box_filename = "./box.pdb"
box_trj = packmol.pack_box(trj_list, [50])
box_trj.save(box_filename)
gaff_mol2_filename1, frcmod_filename1 = amber.run_antechamber("etoh", etoh_filename, charge_method=None)
mol2_filenames = [gaff_mol2_filename1]
frcmod_filenames = [frcmod_filename1]
prmtop_filename = "./out.prmtop"
inpcrd_filename = "./out.inpcrd"
tleap_cmd = amber.build_mixture_prmtop(mol2_filenames, frcmod_filenames, box_filename, prmtop_filename, inpcrd_filename)
print(tleap_cmd)
def test_amber_water_mixture():
water_filename = utils.get_data_filename("chemicals/water/water.mol2")
etoh_filename = utils.get_data_filename("chemicals/etoh/etoh.mol2")
sustiva_filename = utils.get_data_filename(
"chemicals/sustiva/sustiva.mol2")
with utils.enter_temp_directory(
): # Prevents creating tons of GAFF files everywhere.
shutil.copy(water_filename, 'c1.mol2')
shutil.copy(etoh_filename, 'c2.mol2')
shutil.copy(sustiva_filename, 'c3.mol2')
water_filename = 'c1.mol2'
etoh_filename = 'c2.mol2'
sustiva_filename = 'c3.mol2'
#Randomize residue names to avoid clashes
utils.randomize_mol2_residue_names(
[water_filename, etoh_filename, sustiva_filename])
trj0, trj1, trj2 = md.load(water_filename), md.load(
etoh_filename), md.load(sustiva_filename)
trj_list = [trj0, trj1, trj2]
box_filename = "./box.pdb"
box_trj = packmol.pack_box(trj_list, [300, 25, 3])
box_trj.save(box_filename)
gaff_mol2_filename0, frcmod_filename0 = amber.run_antechamber(
"water", water_filename, charge_method=None)
gaff_mol2_filename1, frcmod_filename1 = amber.run_antechamber(
"etoh", etoh_filename, charge_method=None)
gaff_mol2_filename2, frcmod_filename2 = amber.run_antechamber(
"sustiva", sustiva_filename, charge_method=None)
mol2_filenames = [
gaff_mol2_filename0, gaff_mol2_filename1, gaff_mol2_filename2
]
frcmod_filenames = [
frcmod_filename0, frcmod_filename1, frcmod_filename2
]
prmtop_filename = "./out.prmtop"
inpcrd_filename = "./out.inpcrd"
shutil.copy(box_filename, 'renamed.pdb')
tleap_cmd = amber.build_mixture_prmtop(mol2_filenames,
frcmod_filenames, 'renamed.pdb',
prmtop_filename,
inpcrd_filename)
print(tleap_cmd)
#Also do here for case of GAFF water
tleap_cmd = amber.build_mixture_prmtop(mol2_filenames,
frcmod_filenames,
box_filename,
prmtop_filename,
inpcrd_filename,
water_model=None)
print(tleap_cmd)
#Also do here for case of SPC
tleap_cmd = amber.build_mixture_prmtop(mol2_filenames,
frcmod_filenames,
'renamed.pdb',
prmtop_filename,
inpcrd_filename,
water_model='SPC')
print(tleap_cmd)
