5.20. AMBER PRMTOP topology parser¶

Reads an AMBER top file to build the system.

Amber keywords are turned into the following attributes:

 AMBER flag MDAnalysis attribute ATOM_NAME names CHARGE charges ATOMIC_NUMBER elements MASS masses BONDS_INC_HYDROGEN BONDS_WITHOUT_HYDROGEN bonds ANGLES_INC_HYDROGEN ANGLES_WITHOUT_HYDROGEN angles DIHEDRALS_INC_HYDROGEN DIHEDRALS_WITHOUT_HYDROGEN dihedrals / improper ATOM_TYPE_INDEX type_indices AMBER_ATOM_TYPE types RESIDUE_LABEL resnames RESIDUE_POINTER residues

Note

The Amber charge is converted to electron charges as used in MDAnalysis and other packages. To get back Amber charges, multiply by 18.2223.

Chamber-style Amber topologies (i.e. topologies generated via parmed conversion of a CHARMM topology to an AMBER one) are not currently supported. Support will likely be added in future MDAnalysis releases.

5.20.1. Classes¶

class MDAnalysis.topology.TOPParser.TOPParser(filename)[source]

Reads topology information from an AMBER top file.

Reads the following Attributes if in topology: - Atomnames - Charges - Masses - Elements - Atomtypes - Resnames - Type_indices - Bonds - Angles - Dihedrals (inc. impropers)

Guesses the following attributes:
• Elements (if not included in topology)

The format is defined in PARM parameter/topology file specification. The reader tries to detect if it is a newer (AMBER 12?) file format by looking for the flag “ATOMIC_NUMBER”.

Changed in version 0.7.6: parses both amber10 and amber12 formats

Changed in version 0.19.0: parses bonds, angles, dihedrals, and impropers

Changed in version 1.0.0: warns users that chamber-style topologies are not current supported

close()

Close the trajectory file.

convert_forces_from_native(force, inplace=True)

Conversion of forces array force from native to base units

Parameters: force (array_like) – Forces to transform inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input force is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided.

New in version 0.7.7.

convert_forces_to_native(force, inplace=True)

Conversion of force array force from base to native units.

Parameters: force (array_like) – Forces to transform inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input force is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided.

New in version 0.7.7.

convert_pos_from_native(x, inplace=True)

Conversion of coordinate array x from native units to base units.

Parameters: x (array_like) – Positions to transform inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input x is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided.

Changed in version 0.7.5: Keyword inplace can be set to False so that a modified copy is returned unless no conversion takes place, in which case the reference to the unmodified x is returned.

convert_pos_to_native(x, inplace=True)

Conversion of coordinate array x from base units to native units.

Parameters: x (array_like) – Positions to transform inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input x is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided.

Changed in version 0.7.5: Keyword inplace can be set to False so that a modified copy is returned unless no conversion takes place, in which case the reference to the unmodified x is returned.

convert_time_from_native(t, inplace=True)

Convert time t from native units to base units.

Parameters: t (array_like) – Time values to transform inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input t is modified in place and also returned (although note that scalar values t are passed by value in Python and hence an in-place modification has no effect on the caller.) In-place operations improve performance because allocating new arrays is avoided.

Changed in version 0.7.5: Keyword inplace can be set to False so that a modified copy is returned unless no conversion takes place, in which case the reference to the unmodified x is returned.

convert_time_to_native(t, inplace=True)

Convert time t from base units to native units.

Parameters: t (array_like) – Time values to transform inplace (bool, optional) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input t is modified in place and also returned. (Also note that scalar values t are passed by value in Python and hence an in-place modification has no effect on the caller.)

Changed in version 0.7.5: Keyword inplace can be set to False so that a modified copy is returned unless no conversion takes place, in which case the reference to the unmodified x is returned.

convert_velocities_from_native(v, inplace=True)

Conversion of velocities array v from native to base units

Parameters: v (array_like) – Velocities to transform inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input v is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided.

New in version 0.7.5.

convert_velocities_to_native(v, inplace=True)

Conversion of coordinate array v from base to native units

Parameters: v (array_like) – Velocities to transform inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input v is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided.

New in version 0.7.5.

parse(**kwargs)[source]

Parse Amber PRMTOP topology file filename.

Returns: A MDAnalysis Topology object
parse_bonded(num_per_record, numlines)[source]

Extracts bond information from PARM7 format files

Parameters: num_per_record (int) – The number of entries for each record in section numlines (int) – The number of lines to be parsed for this section

Note

For the bond/angle sections of parm7 files, the atom numbers are set to coordinate array index values. As detailed in http://ambermd.org/formats.html to recover the actual atom number, one should divide the values by 3 and add 1. Here, since we want to satisfy zero-indexing, we only divide by 3.

parse_charges(num_per_record, numlines)[source]

Extracts the partial charges for each atom

Parameters: num_per_record (int) – The number of entries for each record in section (unused input) numlines (int) – The number of lines to be parsed in current section attr – A Charges instance containing the partial charges of each atom as defined in the parm7 file Charges
parse_chunks(data, chunksize)[source]

Helper function to parse AMBER PRMTOP bonds/angles.

Parameters: data (list of int) – Input list of the parm7 bond/angle section, zero-indexed num_per_record (int) – The number of entries for each record in the input list vals – A list of tuples containing the atoms involved in a given bonded interaction list of int tuples

Note

In the parm7 format this information is structured in the following format: [ atoms 1:n, internal index ] Where 1:n represent the ids of the n atoms involved in the bond/angle and the internal index links to a given set of FF parameters. Therefore, to extract the required information, we split out the list into chunks of size num_per_record, and only extract the atom ids.

parse_dihedrals(diha, dihh)[source]

Combines hydrogen and non-hydrogen containing AMBER dihedral lists and extracts sublists for conventional dihedrals and improper angles

Parameters: diha (list of tuples) – The atom ids of dihedrals not involving hydrogens dihh (list of tuples) – The atom ids of dihedrals involving hydrogens dihedrals (Dihedrals) – A Dihedrals instance containing a list of all unique dihedrals as defined by the parm7 file impropers (Impropers) – A Impropers instance containing a list of all unique improper dihedrals as defined by the parm7 file

Note

As detailed in http://ambermd.org/formats.html, the dihedral sections of parm7 files contain information about both conventional dihedrals and impropers. The following must be accounted for: 1) If the fourth atom in a dihedral entry is given a negative value, this indicates that it is an improper. 2) If the third atom in a dihedral entry is given a negative value, this indicates that it 1-4 NB interactions are ignored for this dihedrals. This could be due to the dihedral within a ring, or if it is part of a multi-term dihedral definition or if it is an improper.

parse_elements(num_per_record, numlines)[source]

Extracts the atomic numbers of each atom and converts to element type

Parameters: num_per_record (int) – The number of entries for each record in section(unused input) numlines (int) – The number of lines to be pasred in current section attr – A Elements instance containing the element of each atom as defined in the parm7 file Elements

Note

If the record contains atomic numbers <= 0, these will be treated as dummy elements and an attempt will be made to guess the element based on atom type. See issue #2306 for more details.

parse_masses(num_per_record, numlines)[source]

Extracts the mass of each atom

Parameters: num_per_record (int) – The number of entries for each record in section (unused input) numlines (int) – The number of lines to be parsed in current section attr – A Masses instance containing the mass of each atom as defined in the parm7 file Masses
parse_names(num_per_record, numlines)[source]

Extracts atoms names from parm7 file

Parameters: num_per_record (int) – The number of entries for each record in the section (unused input) numlines (int) – The number of lines to be parsed in current section attr – A Atomnames instance containing the names of each atom as defined in the parm7 file Atomnames
parse_residx(num_per_record, numlines)[source]

Extracts the residue pointers for each atom

Parameters: num_per_record (int) – The number of entries for each record in section (unused input) numlines (int) – The number of lines to be parsed in current section vals – A list of zero-formatted residue pointers for each atom list of int
parse_resnames(num_per_record, numlines)[source]

Extracts the names of each residue

Parameters: num_per_record (int) – The number of entries for each recrod in section (unused input) numlines (int) – The number of lines to be parsed in current section attr – A Resnames instance containing the names of each residue as defined in the parm7 file Resnames
parse_type_indices(num_per_record, numlines)[source]

Extracts the index of atom types of the each atom involved in Lennard Jones (6-12) interactions.

Parameters: num_per_record (int) – The number of entries for each record in section (unused input) numlines (int) – The number of lines to be parsed in current section A TypeIndices instance containing the LJ 6-12 atom type index for each atom attr TypeIndices
parse_types(num_per_record, numlines)[source]

Extracts the force field atom types of each atom

Parameters: num_per_record (int) – The number of entries for each record in section (unused input) numlines (int) – The number of lines to be parsed in current section attr – A Atomtypes instance containing the atom types for each atom as defined in the parm7 file Atomtypes
parsesection_mapper(numlines, mapper)[source]

Parses FORTRAN formatted section, and returns a list of all entries in each line

Parameters: numlines (int) – The number of lines to be parsed in this section mapper (lambda operator) – Operator to format entries in current section section – A list of all entries in a given parm7 section list
skipper()[source]

TOPParser :class: helper function, skips lines of input parm7 file until we find the next %FLAG entry and return that

Returns: line – String containing the current line of the parm7 file string