def testProteinLigand(self):
from htmd.builder.solvate import solvate
from parameterize.parameterization.fftype import fftype
from parameterize.parameterization.writers import writeFRCMOD
# Test protein ligand building with parametrized ligand
refdir = home(dataDir=join('test-amber-build', 'protLig'))
tmpdir = os.path.join(self.testDir, 'protLig')
os.makedirs(tmpdir)
mol = Molecule(join(refdir, '3ptb_mod.pdb'))
lig = Molecule(join(refdir, 'benzamidine.pdb'),
guess=('bonds', 'angles', 'dihedrals'))
prm, lig = fftype(lig, method='GAFF2')
writeFRCMOD(lig, prm, join(tmpdir, 'mol.frcmod'))
lig.segid[:] = 'L'
# params =
newmol = Molecule()
newmol.append(lig)
newmol.append(mol)
smol = solvate(newmol)
params = defaultParam() + [
join(tmpdir, 'mol.frcmod'),
]
_ = build(smol, outdir=tmpdir, param=params, ionize=False)
refdir = home(dataDir=join('test-amber-build', 'protLig', 'results'))
_TestAmberBuild._compareResultFolders(refdir, tmpdir, '3PTB')
def _get_prmtop(self):
from parameterize.parameterization.writers import (
writeFRCMOD,
getAtomTypeMapping,
)
with TemporaryDirectory() as tmpDir:
frcFile = os.path.join(tmpDir, "mol.frcmod")
mapping = getAtomTypeMapping(self._parameters)
writeFRCMOD(self.molecule,
self._parameters,
frcFile,
typemap=mapping)
mol2 = self.molecule.copy()
mol2.atomtype[:] = np.vectorize(mapping.get)(mol2.atomtype)
molFile = os.path.join(tmpDir, "mol.mol2")
mol2.write(molFile)
with open(os.path.join(tmpDir, "tleap.inp"), "w") as file:
file.writelines((
"loadAmberParams %s\n" % frcFile,
"MOL = loadMol2 %s\n" % molFile,
"saveAmberParm MOL mol.prmtop mol.inpcrd\n",
"quit",
))
with open(os.path.join(tmpDir, "tleap.out"), "w") as out:
call(("tleap", "-f", "tleap.inp"), cwd=tmpDir, stdout=out)
prmtop = app.AmberPrmtopFile(os.path.join(tmpDir, "mol.prmtop"))
return prmtop