CharmmParameterSet

class simtk.openmm.app.charmmparameterset.CharmmParameterSet(*args, **kwargs)

Stores a parameter set defined by CHARMM files. It stores the equivalent of the information found in the MASS section of the CHARMM topology file (TOP/RTF) and all of the information in the parameter files (PAR)

Parameters:filenames (List of topology, parameter, and stream files to load into the parameter set.) –
The following file type suffixes are recognized. Unrecognized file types raise a TypeError
  • .rtf, .top – Residue topology file
  • .par, .prm – Parameter file
  • .str – Stream file
  • .inp – If “par” is in the file name, it is a parameter file. If
    “top” is in the file name, it is a topology file. Otherwise, raise TypeError
All type lists are dictionaries whose keys are tuples (with however
many elements are needed to define that type of parameter). The types
that can be in any order are SORTED.
- atom_types_str
- atom_types_int
- atom_types_tuple
- bond_types
- angle_types
- urey_bradley_types
- dihedral_types
- improper_types
- cmap_types
- nbfix_types
The dihedral types can be multiterm, so the values for each dict key is
actually a list of DihedralType instances. The atom_types are dicts that
match the name (str), number (int), or (name, number) tuple (tuple) to
the atom type. The tuple is guaranteed to be the most robust, although
when only the integer or string is available the other dictionaries are
helpful

Examples

>>> params = CharmmParameterSet('charmm22.top', 'charmm22.par', 'file.str')
__init__(*args, **kwargs)

Methods

__init__(*args, **kwargs)
condense() This function goes through each of the parameter type dicts and eliminates duplicate types.
loadSet([tfile, pfile, sfiles, permissive]) Instantiates a CharmmParameterSet from a Topology file and a Parameter
readParameterFile(pfile[, permissive]) Reads all of the parameters from a parameter file.
readStreamFile(sfile) Reads RTF and PAR sections from a stream file and dispatches the
readTopologyFile(tfile) Reads _only_ the atom type definitions from a topology file.
classmethod loadSet(tfile=None, pfile=None, sfiles=[], permissive=False)

Instantiates a CharmmParameterSet from a Topology file and a Parameter file (or just a Parameter file if it has all information)

Parameters:
  • tfile (str) – Name of the Topology (RTF/TOP) file
  • pfile (str) – Name of the Parameter (PAR) file
  • sfiles (list of str) – List or tuple of stream (STR) file names.
  • permissive (bool=False) – Accept non-bonbded parameters for undefined atom types
Returns:

New CharmmParameterSet populated with the parameters found in the provided files.

Return type:

CharmmParameterSet

Notes

The RTF file is read first (if provided), followed by the PAR file, followed by the list of stream files (in the order they are provided). Parameters in each stream file will overwrite those that came before (or simply append to the existing set if they are different)

readParameterFile(pfile, permissive=False)

Reads all of the parameters from a parameter file. Versions 36 and later of the CHARMM force field files have an ATOMS section defining all of the atom types. Older versions need to load this information from the RTF/TOP files.

Parameters:
  • pfile (str) – Name of the CHARMM PARameter file to read
  • permissive (bool) – Accept non-bonbded parameters for undefined atom types (default: False).

Notes

The atom types must all be loaded by the end of this routine. Either supply a PAR file with atom definitions in them or read in a RTF/TOP file first. Failure to do so will result in a raised RuntimeError.

readTopologyFile(tfile)

Reads _only_ the atom type definitions from a topology file. This is unnecessary for versions 36 and later of the CHARMM force field.

Parameters:tfile (str) – : Name of the CHARMM TOPology file to read

Notes

The CHARMM TOPology file is also called a Residue Topology File

readStreamFile(sfile)

Reads RTF and PAR sections from a stream file and dispatches the sections to readTopologyFile or readParameterFile

Parameters:sfile (str or CharmmStreamFile) – Stream file to parse
condense()

This function goes through each of the parameter type dicts and eliminates duplicate types. After calling this function, every unique bond, angle, dihedral, improper, or cmap type will pair with EVERY key in the type mapping dictionaries that points to the equivalent type

Example

>>> params = CharmmParameterSet('charmm.prm').condense()
__delattr__

x.__delattr__(‘name’) <==> del x.name

__format__()

default object formatter

__getattribute__

x.__getattribute__(‘name’) <==> x.name

__hash__
__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__
__setattr__

x.__setattr__(‘name’, value) <==> x.name = value

__sizeof__() → int

size of object in memory, in bytes

__str__