def _system_from_amber(self, *receptor_file, **kwargs):
"""
Creates an OpenMM system from the prmtop/inpcrd Amber files
Parameters
----------
receptor_file : list of str
List of filenames corresponding to the prmtop and inpcrd Amber files of the receptor.
Returns
-------
system : openmm.System
prmtop.topology: openmm.Topology
inpcrd.positions: list
List of atomic positions.
total_charge: int
Total charge of the system.
"""
input = {}
for file in receptor_file:
name, ext = utils.parse_ligand_filename(file)
input[ext] = file
prmtop = app.amberprmtopfile.AmberPrmtopFile(input['.prmtop'])
inpcrd = app.amberinpcrdfile.AmberInpcrdFile(input['.inpcrd'])
prm = pmd.amber.AmberParm(input['.prmtop'])
charge = int(floor(0.5 + pmd.tools.netCharge(prm).execute()))
system = prmtop.createSystem(**kwargs)
return self._fix_particle_sigmas(
system), prmtop.topology, inpcrd.positions, charge
def run_antechamber(molecule_name, input_filename, charge_method="bcc", net_charge=None, gaff_mol2_filename=None, frcmod_filename=None,
input_format='mol2', resname=False, log_debug_output=False):
"""Run AmberTools antechamber and parmchk2 to create GAFF mol2 and frcmod files.
Parameters
----------
molecule_name : str
Name of the molecule to be parameterized, will be used in output filenames.
ligand_filename : str
The molecule to be parameterized. Must be tripos mol2 format.
charge_method : str, optional
If not None, the charge method string will be passed to Antechamber.
net_charge : int, optional
If not None, net charge of the molecule to be parameterized.
If None, Antechamber sums up partial charges from the input file.
gaff_mol2_filename : str, optional, default=None
Name of GAFF mol2 filename to output. If None, uses local directory
and molecule_name
frcmod_filename : str, optional, default=None
Name of GAFF frcmod filename to output. If None, uses local directory
and molecule_name
input_format : str, optional, default='mol2'
Format specifier for input file to pass to antechamber.
resname : bool, optional, default=False
Set the residue name used within output files to molecule_name
log_debug_output : bool, optional, default=False
If true, will send output of tleap to logger.
Returns
-------
gaff_mol2_filename : str
GAFF format mol2 filename produced by antechamber
frcmod_filename : str
Amber frcmod file produced by prmchk
"""
utils = import_("openmoltools.utils")
ext = utils.parse_ligand_filename(input_filename)[1]
if gaff_mol2_filename is None:
gaff_mol2_filename = molecule_name + '.gaff.mol2'
if frcmod_filename is None:
frcmod_filename = molecule_name + '.frcmod'
#Build absolute paths for input and output files
gaff_mol2_filename = os.path.abspath( gaff_mol2_filename )
frcmod_filename = os.path.abspath( frcmod_filename )
input_filename = os.path.abspath( input_filename )
def read_file_contents(filename):
infile = open(filename, 'r')
contents = infile.read()
infile.close()
return contents
#Use temporary directory context to do this to avoid issues with spaces in filenames, etc.
with mdtraj.utils.enter_temp_directory():
local_input_filename = 'in.' + input_format
shutil.copy( input_filename, local_input_filename )
# Run antechamber.
cmd = "antechamber -i %(local_input_filename)s -fi %(input_format)s -o out.mol2 -fo mol2 -s 2" % vars()
if charge_method is not None:
cmd += ' -c %s' % charge_method
if net_charge is not None:
cmd += ' -nc %d' % net_charge
if resname:
cmd += ' -rn %s' % molecule_name
if log_debug_output: logger.debug(cmd)
output = getoutput(cmd)
if not os.path.exists('out.mol2'):
msg = "antechamber failed to produce output mol2 file\n"
msg += "command: %s\n" % cmd
msg += "output:\n"
msg += 8 * "----------" + '\n'
msg += output
msg += 8 * "----------" + '\n'
msg += "input mol2:\n"
msg += 8 * "----------" + '\n'
msg += read_file_contents(local_input_filename)
msg += 8 * "----------" + '\n'
raise Exception(msg)
if log_debug_output: logger.debug(output)
# Run parmchk.
cmd = "parmchk2 -i out.mol2 -f mol2 -o out.frcmod"
if log_debug_output: logger.debug(cmd)
output = getoutput(cmd)
if not os.path.exists('out.frcmod'):
msg = "parmchk2 failed to produce output frcmod file\n"
msg += "command: %s\n" % cmd
msg += "output:\n"
msg += 8 * "----------" + '\n'
msg += output
msg += 8 * "----------" + '\n'
msg += "input mol2:\n"
msg += 8 * "----------" + '\n'
msg += read_file_contents('out.mol2')
msg += 8 * "----------" + '\n'
raise Exception(msg)
if log_debug_output: logger.debug(output)
check_for_errors(output)
#Copy back
shutil.copy( 'out.mol2', gaff_mol2_filename )
shutil.copy( 'out.frcmod', frcmod_filename )
return gaff_mol2_filename, frcmod_filename
def run_antechamber(molecule_name, input_filename, charge_method="bcc", net_charge=None, gaff_mol2_filename=None, frcmod_filename=None):
"""Run AmberTools antechamber and parmchk2 to create GAFF mol2 and frcmod files.
Parameters
----------
molecule_name : str
Name of the molecule to be parameterized, will be used in output filenames.
ligand_filename : str
The molecule to be parameterized. Must be tripos mol2 format.
charge_method : str, optional
If not None, the charge method string will be passed to Antechamber.
net_charge : int, optional
If not None, net charge of the molecule to be parameterized.
If None, Antechamber sums up partial charges from the input file.
gaff_mol2_filename : str, optional, default=None
Name of GAFF mol2 filename to output. If None, uses local directory
and molecule_name
frcmod_filename : str, optional, default=None
Name of GAFF frcmod filename to output. If None, uses local directory
and molecule_name
Returns
-------
gaff_mol2_filename : str
GAFF format mol2 filename produced by antechamber
frcmod_filename : str
Amber frcmod file produced by prmchk
"""
utils = import_("openmoltools.utils")
ext = utils.parse_ligand_filename(input_filename)[1]
filetype = ext[1:]
if filetype != "mol2":
raise(ValueError("Must input mol2 filename"))
if gaff_mol2_filename is None:
gaff_mol2_filename = molecule_name + '.gaff.mol2'
if frcmod_filename is None:
frcmod_filename = molecule_name + '.frcmod'
#Build absolute paths for input and output files
gaff_mol2_filename = os.path.abspath( gaff_mol2_filename )
frcmod_filename = os.path.abspath( frcmod_filename )
input_filename = os.path.abspath( input_filename )
#Use temporary directory context to do this to avoid issues with spaces in filenames, etc.
with mdtraj.utils.enter_temp_directory():
shutil.copy( input_filename, 'in.mol2' )
cmd = "antechamber -i in.mol2 -fi mol2 -o out.mol2 -fo mol2 -s 2"
if charge_method is not None:
cmd += ' -c %s' % charge_method
if net_charge is not None:
cmd += ' -nc %d' % net_charge
logger.debug(cmd)
output = getoutput(cmd)
logger.debug(output)
cmd = "parmchk2 -i out.mol2 -f mol2 -o out.frcmod"
logger.debug(cmd)
output = getoutput(cmd)
logger.debug(output)
check_for_errors( output )
#Copy back
shutil.copy( 'out.mol2', gaff_mol2_filename )
shutil.copy( 'out.frcmod', frcmod_filename )
return gaff_mol2_filename, frcmod_filename
def run_antechamber(molecule_name, input_filename, charge_method="bcc", net_charge=None, gaff_mol2_filename=None, frcmod_filename=None,
input_format='mol2', resname=False, log_debug_output=False):
"""Run AmberTools antechamber and parmchk2 to create GAFF mol2 and frcmod files.
Parameters
----------
molecule_name : str
Name of the molecule to be parameterized, will be used in output filenames.
ligand_filename : str
The molecule to be parameterized. Must be tripos mol2 format.
charge_method : str, optional
If not None, the charge method string will be passed to Antechamber.
net_charge : int, optional
If not None, net charge of the molecule to be parameterized.
If None, Antechamber sums up partial charges from the input file.
gaff_mol2_filename : str, optional, default=None
Name of GAFF mol2 filename to output. If None, uses local directory
and molecule_name
frcmod_filename : str, optional, default=None
Name of GAFF frcmod filename to output. If None, uses local directory
and molecule_name
input_format : str, optional, default='mol2'
Format specifier for input file to pass to antechamber.
resname : bool, optional, default=False
Set the residue name used within output files to molecule_name
log_debug_output : bool, optional, default=False
If true, will send output of tleap to logger.
Returns
-------
gaff_mol2_filename : str
GAFF format mol2 filename produced by antechamber
frcmod_filename : str
Amber frcmod file produced by prmchk
"""
utils = import_("openmoltools.utils")
ext = utils.parse_ligand_filename(input_filename)[1]
if gaff_mol2_filename is None:
gaff_mol2_filename = molecule_name + '.gaff.mol2'
if frcmod_filename is None:
frcmod_filename = molecule_name + '.frcmod'
#Build absolute paths for input and output files
gaff_mol2_filename = os.path.abspath( gaff_mol2_filename )
frcmod_filename = os.path.abspath( frcmod_filename )
input_filename = os.path.abspath( input_filename )
def read_file_contents(filename):
infile = open(filename, 'r')
contents = infile.read()
infile.close()
return contents
#Use temporary directory context to do this to avoid issues with spaces in filenames, etc.
with mdtraj.utils.enter_temp_directory():
local_input_filename = 'in.' + input_format
shutil.copy( input_filename, local_input_filename )
# Run antechamber.
cmd = "antechamber -i %(local_input_filename)s -fi %(input_format)s -o out.mol2 -fo mol2 -s 2" % vars()
if charge_method is not None:
cmd += ' -c %s' % charge_method
if net_charge is not None:
cmd += ' -nc %d' % net_charge
if resname:
cmd += ' -rn %s' % molecule_name
if log_debug_output: logger.debug(cmd)
output = getoutput(cmd)
if not os.path.exists('out.mol2'):
msg = "antechamber failed to produce output mol2 file\n"
msg += "command: %s\n" % cmd
msg += "output:\n"
msg += 8 * "----------" + '\n'
msg += output
msg += 8 * "----------" + '\n'
msg += "input mol2:\n"
msg += 8 * "----------" + '\n'
msg += read_file_contents(local_input_filename)
msg += 8 * "----------" + '\n'
raise Exception(msg)
if log_debug_output: logger.debug(output)
# Run parmchk.
cmd = "parmchk2 -i out.mol2 -f mol2 -o out.frcmod"
if log_debug_output: logger.debug(cmd)
output = getoutput(cmd)
if not os.path.exists('out.frcmod'):
msg = "parmchk2 failed to produce output frcmod file\n"
msg += "command: %s\n" % cmd
msg += "output:\n"
msg += 8 * "----------" + '\n'
msg += output
msg += 8 * "----------" + '\n'
msg += "input mol2:\n"
msg += 8 * "----------" + '\n'
msg += read_file_contents('out.mol2')
msg += 8 * "----------" + '\n'
raise Exception(msg)
if log_debug_output: logger.debug(output)
check_for_errors(output)
#Copy back
shutil.copy( 'out.mol2', gaff_mol2_filename )
shutil.copy( 'out.frcmod', frcmod_filename )
return gaff_mol2_filename, frcmod_filename
def run_antechamber(molecule_name,
input_filename,
charge_method="bcc",
net_charge=None,
gaff_mol2_filename=None,
frcmod_filename=None):
"""Run AmberTools antechamber and parmchk2 to create GAFF mol2 and frcmod files.
Parameters
----------
molecule_name : str
Name of the molecule to be parameterized, will be used in output filenames.
ligand_filename : str
The molecule to be parameterized. Must be tripos mol2 format.
charge_method : str, optional
If not None, the charge method string will be passed to Antechamber.
net_charge : int, optional
If not None, net charge of the molecule to be parameterized.
If None, Antechamber sums up partial charges from the input file.
gaff_mol2_filename : str, optional, default=None
Name of GAFF mol2 filename to output. If None, uses local directory
and molecule_name
frcmod_filename : str, optional, default=None
Name of GAFF frcmod filename to output. If None, uses local directory
and molecule_name
Returns
-------
gaff_mol2_filename : str
GAFF format mol2 filename produced by antechamber
frcmod_filename : str
Amber frcmod file produced by prmchk
"""
utils = import_("openmoltools.utils")
ext = utils.parse_ligand_filename(input_filename)[1]
filetype = ext[1:]
if filetype != "mol2":
raise (ValueError("Must input mol2 filename"))
if gaff_mol2_filename is None:
gaff_mol2_filename = molecule_name + '.gaff.mol2'
if frcmod_filename is None:
frcmod_filename = molecule_name + '.frcmod'
#Build absolute paths for input and output files
gaff_mol2_filename = os.path.abspath(gaff_mol2_filename)
frcmod_filename = os.path.abspath(frcmod_filename)
input_filename = os.path.abspath(input_filename)
#Use temporary directory context to do this to avoid issues with spaces in filenames, etc.
with mdtraj.utils.enter_temp_directory():
shutil.copy(input_filename, 'in.mol2')
cmd = "antechamber -i in.mol2 -fi mol2 -o out.mol2 -fo mol2 -s 2"
if charge_method is not None:
cmd += ' -c %s' % charge_method
if net_charge is not None:
cmd += ' -nc %d' % net_charge
logger.debug(cmd)
output = getoutput(cmd)
logger.debug(output)
cmd = "parmchk2 -i out.mol2 -f mol2 -o out.frcmod"
logger.debug(cmd)
output = getoutput(cmd)
logger.debug(output)
check_for_errors(output)
#Copy back
shutil.copy('out.mol2', gaff_mol2_filename)
shutil.copy('out.frcmod', frcmod_filename)
return gaff_mol2_filename, frcmod_filename