def test_run_antechamber_charges():
molecule_name = "acetate"
input_filename = utils.get_data_filename("chemicals/acetate/acetate.mol2")
with utils.enter_temp_directory(): # Prevents creating tons of GAFF files everywhere.
gaff_mol2_filename, frcmod_filename = utils.run_antechamber(
molecule_name, input_filename, charge_method=None, net_charge=-1
)
def generate_ff(molecule_name, infile, mol2_filename, ff_mod, topfile):
convert_molecule(infile,mol2_filename)
gaff_mol2_filename, frcmod_filename = run_antechamber(molecule_name, mol2_filename, charge_method="bcc")
ffxml = create_ffxml_file(gaff_mol2_filename, frcmod_filename)
forcefield = app.ForceField(ffxml)
if ff_mod == True:
ff_mod_funct(forcefield, topfile)
return forcefield
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 = utils.run_antechamber(molecule_name, input_filename, charge_method=None)
prmtop, inpcrd = utils.run_tleap(molecule_name, gaff_mol2_filename, frcmod_filename)
#!/usr/bin/env python
import sys
from gaff2xml.utils import run_antechamber
if __name__ == "__main__":
if len(sys.argv) <= 1:
print("""Usage: generate_example_data.py ligand_name
Note: this should be run in the gaff2xml/chemicals/ligand_name directory.
""")
else:
molecule_name, mol2_filename = sys.argv[1:]
run_antechamber(molecule_name, mol2_filename, charge_model="bcc")
