CharmmParameterSet¶
- class 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)¶
Initialize self. See help(type(self)) for accurate signature.
Methods
__init__(*args, **kwargs)Initialize self.
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 file (or just a Parameter file if it has all information)
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 sections to readTopologyFile or readParameterFile
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
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()
