def test_gromacs_merge():
etoh_filename = utils.get_data_filename("chemicals/etoh/etoh.mol2")
benzene_filename = utils.get_data_filename("chemicals/benzene/benzene.mol2")
with utils.enter_temp_directory(): #Prevents creating lots of tleap/antechamber files everywhere
#Generate frcmod files, mol2 files
gaff_mol2_filename1, frcmod_filename1 = amber.run_antechamber( "etoh", etoh_filename, charge_method = None)
gaff_mol2_filename2, frcmod_filename2 = amber.run_antechamber( "benzene", benzene_filename, charge_method = None)
#Set file names
prmtop_filename1 = "./out1.prmtop"
prmtop_filename2 = "./out2.prmtop"
crd_filename1 = "./out1.inpcrd"
crd_filename2 = "./out2.inpcrd"
top_filename1 = "./out1.top"
top_filename2 = "./out2.top"
gro_filename1 = "./out1.gro"
gro_filename2 = "./out2.gro"
#Generate AMBER files
amber.run_tleap( 'etoh', gaff_mol2_filename1, frcmod_filename1, prmtop_filename1, crd_filename1 )
amber.run_tleap( 'benzene', gaff_mol2_filename2, frcmod_filename2, prmtop_filename2, crd_filename2 )
#Convert to GROMACS
utils.amber_to_gromacs( "etoh", prmtop_filename1, crd_filename1, out_top = top_filename1, out_gro = gro_filename1 )
utils.amber_to_gromacs( "benzene", prmtop_filename2, crd_filename2, out_top = top_filename2, out_gro = gro_filename2 )
#Merge topologies
gromacs.merge_topologies( [ top_filename1, top_filename2], './combined.top', 'combined', molecule_numbers = [1, 5], molecule_names = ['etoh', 'benzene'] )
#Test editing of molecule numbers in topology file
gromacs.change_molecules_section( './combined.top', './edited.top', ['etoh', 'benzene'], [10, 20] )
def test_gromacs_merge():
etoh_filename = utils.get_data_filename("chemicals/etoh/etoh.mol2")
benzene_filename = utils.get_data_filename("chemicals/benzene/benzene.mol2")
with utils.enter_temp_directory(): #Prevents creating lots of tleap/antechamber files everywhere
#Generate frcmod files, mol2 files
gaff_mol2_filename1, frcmod_filename1 = amber.run_antechamber( "etoh", etoh_filename, charge_method = None)
gaff_mol2_filename2, frcmod_filename2 = amber.run_antechamber( "benzene", benzene_filename, charge_method = None)
#Set file names
prmtop_filename1 = "./out1.prmtop"
prmtop_filename2 = "./out2.prmtop"
crd_filename1 = "./out1.inpcrd"
crd_filename2 = "./out2.inpcrd"
top_filename1 = "./out1.top"
top_filename2 = "./out2.top"
gro_filename1 = "./out1.gro"
gro_filename2 = "./out2.gro"
#Generate AMBER files
amber.run_tleap( 'etoh', gaff_mol2_filename1, frcmod_filename1, prmtop_filename1, crd_filename1 )
amber.run_tleap( 'benzene', gaff_mol2_filename2, frcmod_filename2, prmtop_filename2, crd_filename2 )
#Convert to GROMACS
utils.convert_via_acpype( "etoh", prmtop_filename1, crd_filename1, out_top = top_filename1, out_gro = gro_filename1 )
utils.convert_via_acpype( "benzene", prmtop_filename2, crd_filename2, out_top = top_filename2, out_gro = gro_filename2 )
#Merge topologies
gromacs.merge_topologies( [ top_filename1, top_filename2], './combined.top', 'combined', molecule_numbers = [1, 5], molecule_names = ['etoh', 'benzene'] )
#Test editing of molecule numbers in topology file
gromacs.change_molecules_section( './combined.top', './edited.top', ['etoh', 'benzene'], [10, 20] )
def test_gromacs_solvate():
etoh_filename = utils.get_data_filename("chemicals/etoh/etoh.mol2")
with utils.enter_temp_directory(): #Prevents creating lots of tleap/antechamber files everywhere
#Generate frcmod files, mol2 files
gaff_mol2_filename, frcmod_filename = amber.run_antechamber( "etoh", etoh_filename, charge_method = None)
#Amber setup
amber.run_tleap( 'etoh', gaff_mol2_filename, frcmod_filename, 'etoh.prmtop', 'etoh.crd' )
#GROMACS conversion
utils.amber_to_gromacs( 'etoh', 'etoh.prmtop', 'etoh.crd', 'etoh.top', 'etoh.gro' )
#Solvate
gromacs.do_solvate( 'etoh.top', 'etoh.gro', 'etoh_solvated.top', 'etoh_solvated.gro', 1.2, 'dodecahedron', 'spc216', 'tip3p.itp' )
def test_gromacs_solvate():
etoh_filename = utils.get_data_filename("chemicals/etoh/etoh.mol2")
with utils.enter_temp_directory(): #Prevents creating lots of tleap/antechamber files everywhere
#Generate frcmod files, mol2 files
gaff_mol2_filename, frcmod_filename = amber.run_antechamber( "etoh", etoh_filename, charge_method = None)
#Amber setup
amber.run_tleap( 'etoh', gaff_mol2_filename, frcmod_filename, 'etoh.prmtop', 'etoh.crd' )
#GROMACS conversion
utils.convert_via_acpype( 'etoh', 'etoh.prmtop', 'etoh.crd', 'etoh.top', 'etoh.gro' )
#Solvate
gromacs.do_solvate( 'etoh.top', 'etoh.gro', 'etoh_solvated.top', 'etoh_solvated.gro', 1.2, 'dodecahedron', 'spc216', 'tip3p.itp' )
def test_acpype_conversion():
molecule_name = 'sustiva'
input_filename = utils.get_data_filename("chemicals/sustiva/sustiva.mol2")
with utils.enter_temp_directory(): # Prevents creating tons of GAFF files everywhere.
gaff_mol2_filename, frcmod_filename = amber.run_antechamber(molecule_name, input_filename, charge_method=None)
prmtop, inpcrd = amber.run_tleap(molecule_name, gaff_mol2_filename, frcmod_filename)
out_top, out_gro = utils.convert_via_acpype( molecule_name, prmtop, inpcrd )
def test_run_tleap():
molecule_name = "sustiva"
input_filename = utils.get_data_filename("chemicals/sustiva/sustiva.mol2")
with utils.enter_temp_directory(
): # Prevents creating tons of GAFF files everywhere.
gaff_mol2_filename, frcmod_filename = amber.run_antechamber(
molecule_name, input_filename, charge_method=None)
prmtop, inpcrd = amber.run_tleap(molecule_name, gaff_mol2_filename,
frcmod_filename)
def test_acpype_conversion():
molecule_name = 'sustiva'
input_filename = utils.get_data_filename("chemicals/sustiva/sustiva.mol2")
with utils.enter_temp_directory(
): # Prevents creating tons of GAFF files everywhere.
gaff_mol2_filename, frcmod_filename = amber.run_antechamber(
molecule_name, input_filename, charge_method=None)
prmtop, inpcrd = amber.run_tleap(molecule_name, gaff_mol2_filename,
frcmod_filename)
out_top, out_gro = utils.convert_via_acpype(molecule_name, prmtop,
inpcrd)
def generate_amber_files(self, ligand_name, file):
"""
Generates the prmtop and inpcrd files for a ligand.
Parameters
----------
ligand_name : str
The name of the ligand.
file : str
Mol2 file of the ligand.
Returns
-------
prmtop_filename : str
Amber prmtop file produced by tleap.
inpcrd_filename : str
Amber inpcrd file produced by tleap.
"""
gaff_mol2_filename1, frcmod_filename1 = amber.run_antechamber(
ligand_name, file, resname=True, charge_method=None)
source_mol2 = os.path.abspath(gaff_mol2_filename1)
source_frcmod = os.path.abspath(frcmod_filename1)
destination = os.path.abspath('data')
shutil.move(source_mol2,
os.path.join(destination, os.path.basename(source_mol2)))
shutil.move(source_frcmod,
os.path.join(destination, os.path.basename(source_frcmod)))
amber.run_tleap(
ligand_name,
os.path.join(destination, os.path.basename(source_mol2)),
os.path.join(destination, os.path.basename(source_frcmod)),
f'{ligand_name}.prmtop', f'{ligand_name}.inpcrd')
source_prmtop = os.path.abspath(f'{ligand_name}.prmtop')
source_inpcrd = os.path.abspath(f'{ligand_name}.inpcrd')
shutil.move(source_prmtop,
os.path.join(destination, os.path.basename(source_prmtop)))
shutil.move(source_inpcrd,
os.path.join(destination, os.path.basename(source_inpcrd)))
return os.path.join(destination,
os.path.basename(source_prmtop)), os.path.join(
destination, os.path.basename(source_inpcrd))
def test_parmed_conversion():
molecule_name = 'sustiva'
input_filename = utils.get_data_filename("chemicals/sustiva/sustiva.mol2")
with utils.enter_temp_directory(
): # Prevents creating tons of GAFF files everywhere.
#Make sure conversion runs
gaff_mol2_filename, frcmod_filename = amber.run_antechamber(
molecule_name, input_filename, charge_method=None)
prmtop, inpcrd = amber.run_tleap(molecule_name, gaff_mol2_filename,
frcmod_filename)
out_top, out_gro = utils.amber_to_gromacs(molecule_name,
prmtop,
inpcrd,
precision=8)
#Test energies before and after conversion
#Set up amber system
a = parmed.amber.AmberParm(prmtop, inpcrd)
ambersys = a.createSystem()
ambercon = mmmm.Context(ambersys, mm.VerletIntegrator(0.001))
ambercon.setPositions(a.positions)
#Set up GROMACS system
g = parmed.load_file(out_top)
gro = parmed.gromacs.GromacsGroFile.parse(out_gro)
g.box = gro.box
g.positions = gro.positions
gromacssys = g.createSystem()
gromacscon = mmmm.Context(gromacssys, mm.VerletIntegrator(0.001))
gromacscon.setPositions(g.positions)
#Check energies
a_energies = parmed.openmm.utils.energy_decomposition(a, ambercon)
g_energies = parmed.openmm.utils.energy_decomposition(g, gromacscon)
#Check components
tolerance = 1e-5
ok = True
for key in a_energies.keys():
diff = np.abs(a_energies[key] - g_energies[key])
if diff / np.abs(a_energies[key]) > tolerance:
ok = False
print(
"In testing AMBER to GROMACS conversion, %s energy differs by %.5g, which is more than a fraction %.2g of the total, so conversion appears not to be working properly."
% (key, diff, tolerance))
if not ok:
raise (ValueError(
"AMBER to GROMACS conversion yields energies which are too different."
))
def test_parmed_conversion():
molecule_name = 'sustiva'
input_filename = utils.get_data_filename("chemicals/sustiva/sustiva.mol2")
with utils.enter_temp_directory(): # Prevents creating tons of GAFF files everywhere.
#Make sure conversion runs
gaff_mol2_filename, frcmod_filename = amber.run_antechamber(molecule_name, input_filename, charge_method=None)
prmtop, inpcrd = amber.run_tleap(molecule_name, gaff_mol2_filename, frcmod_filename)
out_top, out_gro = utils.amber_to_gromacs( molecule_name, prmtop, inpcrd, precision = 8 )
#Test energies before and after conversion
#Set up amber system
a = parmed.amber.AmberParm( prmtop, inpcrd )
ambersys = a.createSystem()
ambercon = mmmm.Context( ambersys, mm.VerletIntegrator(0.001))
ambercon.setPositions( a.positions )
#Set up GROMACS system
g = parmed.load_file( out_top )
gro = parmed.gromacs.GromacsGroFile.parse( out_gro )
g.box = gro.box
g.positions = gro.positions
gromacssys = g.createSystem()
gromacscon = mmmm.Context( gromacssys, mm.VerletIntegrator(0.001))
gromacscon.setPositions( g.positions )
#Check energies
a_energies = parmed.openmm.utils.energy_decomposition( a, ambercon )
g_energies = parmed.openmm.utils.energy_decomposition( g, gromacscon )
#Check components
tolerance = 1e-5
ok = True
for key in a_energies.keys():
diff = np.abs(a_energies[key] - g_energies[key] )
if diff/np.abs(a_energies[key]) > tolerance:
ok = False
print("In testing AMBER to GROMACS conversion, %s energy differs by %.5g, which is more than a fraction %.2g of the total, so conversion appears not to be working properly." % ( key, diff, tolerance) )
if not ok:
raise(ValueError("AMBER to GROMACS conversion yields energies which are too different."))
def test_run_tleap():
molecule_name = "sustiva"
input_filename = utils.get_data_filename("chemicals/sustiva/sustiva.mol2")
with utils.enter_temp_directory(): # Prevents creating tons of GAFF files everywhere.
gaff_mol2_filename, frcmod_filename = amber.run_antechamber(molecule_name, input_filename, charge_method=None)
prmtop, inpcrd = amber.run_tleap(molecule_name, gaff_mol2_filename, frcmod_filename)
def gcrt2prmtop(gcrt_file):
system_name=gcrt_file.split('.')[0]
amber.run_antechamber(system_name, gcrt_file, charge_method=None, input_format='gcrt')
amber.run_tleap(system_name, system_name+'.gaff.mol2',system_name+'.frcmod',system_name+'.prmtop',system_name+'.crd')
return None
