Ejemplo n.º 1
0
    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
Ejemplo n.º 2
0
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
Ejemplo n.º 3
0
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
Ejemplo n.º 4
0
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
Ejemplo n.º 5
0
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