def fftype(mol,
rtfFile=None,
prmFile=None,
method='GAFF2',
acCharges=None,
tmpDir=None,
netcharge=None):
"""
Assing atom types and force field parameters for a given molecule.
Additionally, atom masses and improper dihedral are set.
Optionally, atom charges can be set if `acCharges` is set (see below).
The assignment can be done:
1. For CHARMM CGenFF_2b6 with MATCH (method = 'CGenFF_2b6');
2. For AMBER GAFF with antechamber (method = 'GAFF');
3. For AMBER GAFF2 with antechamber (method = 'GAFF2');
Parameters
----------
mol : Molecule
Molecule to use for the assignment
rtfFile : str
Path to a RTF file from which to read the topology
prmFile : str
Path to a PRM file from which to read the parameters
method : str
Atomtyping assignment method.
Use :func:`fftype.listFftypemethods <htmd.parameterization.fftype.listFftypemethods>` to get a list of available
methods.
Default: :func:`fftype.defaultFftypemethod <htmd.parameterization.fftype.defaultFftypemethod>`
acCharges : str
Optionally assign charges with antechamber. Check `antechamber -L` for available options.
Note: only works for GAFF and GAFF2.
tmpDir: str
Directory for temporary files. If None, a directory is created and
deleted automatically.
netcharge : float
The net charge of the molecule.
Returns
-------
prm : :class:`ParameterSet <parmed.parameters.ParameterSet>` object
Returns a parmed ParameterSet object with the parameters.
mol : :class:`Molecule <htmd.molecule.molecule.Molecule>` object
The modified Molecule object with the matching atom types for the ParameterSet
"""
import parmed
if method not in fftypemethods:
raise ValueError('Invalid method {}. Available methods {}'.format(
method, ','.join(fftypemethods)))
if method == 'CGenFF_2b6' and acCharges:
raise ValueError('acCharges')
if netcharge is None:
netcharge = int(round(np.sum(mol.charge)))
logger.warning(
'Molecular charge is set to {} by adding up the atomic charges'.
format(netcharge))
if rtfFile and prmFile:
from htmd.parameterization.readers import readRTF
logger.info('Reading FF parameters from {} and {}'.format(
rtfFile, prmFile))
prm = parmed.charmm.CharmmParameterSet(rtfFile, prmFile)
names, elements, atomtypes, charges, masses, impropers = readRTF(
rtfFile)
else:
logger.info('Assigning atom types with {}'.format(method))
renamed_mol = _canonicalizeAtomNames(mol)
# Create a temporary directory
with TemporaryDirectory() as tmpdir:
# HACK to keep the files
tmpdir = tmpdir if tmpDir is None else tmpDir
logger.debug('Temporary directory: {}'.format(tmpdir))
if method in ('GAFF', 'GAFF2'):
from htmd.molecule.molecule import Molecule
from htmd.parameterization.readers import readPREPI, readFRCMOD
# Write the molecule to a file
renamed_mol.write(os.path.join(tmpdir, 'mol.mol2'))
atomtype = method.lower()
# Set arguments
cmd = [
'antechamber', '-at', atomtype, '-nc',
str(netcharge), '-fi', 'mol2', '-i', 'mol.mol2', '-fo',
'prepi', '-o', 'mol.prepi'
]
if acCharges is not None:
cmd += ['-c', acCharges]
# Run antechamber
with TemporaryFile() as stream:
if subprocess.call(
cmd, cwd=tmpdir, stdout=stream,
stderr=stream) != 0:
raise RuntimeError('"antechamber" failed')
stream.seek(0)
for line in stream.readlines():
logger.debug(line)
# Set arguments
cmd = [
'parmchk2', '-f', 'prepi', '-s', atomtype, '-i',
'mol.prepi', '-o', 'mol.frcmod', '-a', 'Y'
]
# Run parmchk2
with TemporaryFile() as stream:
if subprocess.call(
cmd, cwd=tmpdir, stdout=stream,
stderr=stream) != 0:
raise RuntimeError('"parmchk2" failed')
stream.seek(0)
for line in stream.readlines():
logger.debug(line)
# Check if antechamber did changes in atom names (and suggest the user to fix the names)
acmol = Molecule(os.path.join(tmpdir, 'NEWPDB.PDB'),
type='pdb')
acmol.name = np.array([n.upper()
for n in acmol.name]).astype(np.object)
changed_mol_acmol = np.setdiff1d(renamed_mol.name, acmol.name)
changed_acmol_mol = np.setdiff1d(acmol.name, renamed_mol.name)
if len(changed_mol_acmol) != 0 or len(changed_acmol_mol) != 0:
raise RuntimeError(
'Initial atom names {} were changed by antechamber to {}. '
'This probably means that the start of the atom name does not match '
'element symbol. '
'Please check the molecule.'
''.format(','.join(changed_mol_acmol),
','.join(changed_acmol_mol)))
# Read the results
prm = parmed.amber.AmberParameterSet(
os.path.join(tmpdir, 'mol.frcmod'))
names, atomtypes, charges, impropers = readPREPI(
renamed_mol, os.path.join(tmpdir, 'mol.prepi'))
masses, elements = readFRCMOD(
atomtypes, os.path.join(tmpdir, 'mol.frcmod'))
elif method == 'CGenFF_2b6':
from htmd.parameterization.readers import readRTF
# Write the molecule to a file
renamed_mol.write(os.path.join(tmpdir, 'mol.pdb'))
# Set arguments
cmd = [
'match-typer', '-charge',
str(netcharge), '-forcefield', 'top_all36_cgenff_new',
'mol.pdb'
]
# Run match-type
with TemporaryFile() as stream:
if subprocess.call(
cmd, cwd=tmpdir, stdout=stream,
stderr=stream) != 0:
raise RuntimeError('"match-typer" failed')
stream.seek(0)
for line in stream.readlines():
logger.debug(line)
prm = parmed.charmm.CharmmParameterSet(
os.path.join(tmpdir, 'mol.rtf'),
os.path.join(tmpdir, 'mol.prm'))
names, elements, atomtypes, charges, masses, impropers = readRTF(
os.path.join(tmpdir, 'mol.rtf'))
else:
raise ValueError('Invalid method {}'.format(method))
assert np.all(renamed_mol.name == names)
assert np.all(mol.element == elements)
mol = mol.copy()
mol.atomtype = atomtypes
mol.masses = masses
mol.impropers = impropers
if acCharges is not None:
mol.charge = charges
return prm, mol
def fftype(mol,
rtfFile=None,
prmFile=None,
method=FFTypeMethod.CGenFF_2b6,
acCharges=None,
tmpDir=None,
netcharge=None):
"""
Function to assign atom types and force field parameters for a given molecule.
The assigment can be done:
1. For CHARMM CGenFF_2b6 with MATCH (method = FFTypeMethod.CGenFF_2b6);
2. For AMBER GAFF with antechamber (method = FFTypeMethod.GAFF);
3. For AMBER GAFF2 with antechamber (method = FFTypeMethod.GAFF2);
Parameters
----------
mol : FFMolecule
Molecule to use for the assigment
rtfFile : str
Path to a RTF file from which to read the topology
prmFile : str
Path to a PRM file from which to read the parameters
method : FFTypeMethod
Assigment method
acCharges : str
Optionally assign charges with antechamber. Check `antechamber -L` for available options. Caution: This will
overwrite any charges defined in the mol2 file.
tmpDir: str
Directory for temporary files. If None, a directory is created and
deleted automatically.
netcharge : float
The net charge of the molecule.
Returns
-------
prm : :class:`ParameterSet<parmed.parameters.ParameterSet>` object
Returns a parmed ParameterSet object with the parameters.
mol : :class:`Molecule <htmd.molecule.molecule.Molecule>` object
The modified Molecule object with the matching atom types for the ParameterSet
"""
if netcharge is None:
netcharge = np.sum(mol.charge)
netcharge = int(round(netcharge))
if rtfFile and prmFile:
logger.info('Reading FF parameters from {} and {}'.format(
rtfFile, prmFile))
prm = parmed.charmm.CharmmParameterSet(rtfFile, prmFile)
names, elements, atomtypes, charges, masses, impropers = readRTF(
rtfFile)
# addParmedResidue(prm, names, elements, atomtypes, charges, impropers)
else:
logger.info('Assigned atom types with {}'.format(method.name))
# Find the executables
if method == FFTypeMethod.GAFF or method == FFTypeMethod.GAFF2:
antechamber_binary = shutil.which("antechamber")
if not antechamber_binary:
raise RuntimeError("antechamber executable not found")
parmchk2_binary = shutil.which("parmchk2")
if not parmchk2_binary:
raise RuntimeError("parmchk2 executable not found")
elif method == FFTypeMethod.CGenFF_2b6:
match_binary = shutil.which("match-typer")
if not match_binary:
raise RuntimeError("match-typer executable not found")
else:
raise ValueError('method')
# Create a temporary directory
with TemporaryDirectory() as tmpdir:
# HACK to keep the files
tmpdir = tmpdir if tmpDir is None else tmpDir
if method == FFTypeMethod.GAFF or method == FFTypeMethod.GAFF2:
# Write the molecule to a file
mol.write(os.path.join(tmpdir, 'mol.mol2'))
# Run antechamber
if method == FFTypeMethod.GAFF:
atomtype = "gaff"
elif method == FFTypeMethod.GAFF2:
atomtype = "gaff2"
else:
raise ValueError('method')
cmd = [
antechamber_binary, '-at', atomtype, '-nc',
str(netcharge), '-fi', 'mol2', '-i', 'mol.mol2', '-fo',
'prepi', '-o', 'mol.prepi'
]
if acCharges is not None:
cmd += ['-c', acCharges]
returncode = subprocess.call(cmd, cwd=tmpdir)
if returncode != 0:
raise RuntimeError('"antechamber" failed')
# Run parmchk2
returncode = subprocess.call([
parmchk2_binary, '-f', 'prepi', '-i', 'mol.prepi', '-o',
'mol.frcmod', '-a', 'Y'
],
cwd=tmpdir)
if returncode != 0:
raise RuntimeError('"parmchk2" failed')
# Read the results
prm = parmed.amber.AmberParameterSet(
os.path.join(tmpdir, 'mol.frcmod'))
names, elements, atomtypes, charges, masses, impropers = readPREPI(
mol, os.path.join(tmpdir, 'mol.prepi'))
# addParmedResidue(prm, names, elements, atomtypes, charges, impropers)
elif method == FFTypeMethod.CGenFF_2b6:
# Write the molecule to a file
mol.write(os.path.join(tmpdir, 'mol.pdb'))
# Run match-type
returncode = subprocess.call([
match_binary, '-charge',
str(netcharge), '-forcefield', 'top_all36_cgenff_new',
'mol.pdb'
],
cwd=tmpdir)
if returncode != 0:
raise RuntimeError('"match-typer" failed')
prm = parmed.charmm.CharmmParameterSet(
os.path.join(tmpdir, 'mol.rtf'),
os.path.join(tmpdir, 'mol.prm'))
names, elements, atomtypes, charges, masses, impropers = readRTF(
os.path.join(tmpdir, 'mol.rtf'))
# addParmedResidue(prm, names, elements, atomtypes, charges, impropers)
else:
raise ValueError('Invalide method {}'.format(method))
# Substituting values from the read-in topology
mol.name = names
mol.element = elements
mol.atomtype = atomtypes
mol.charge = charges
mol.impropers = impropers
if len(mol.masses) == 0:
mol.masses = masses
return prm, mol