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htmd.builder.charmm module#

htmd.builder.charmm.build(mol, topo=None, param=None, stream=None, prefix='structure', outdir='./build', caps=None, ionize=True, saltconc=0, saltanion=None, saltcation=None, disulfide=None, regenerate=['angles', 'dihedrals'], patches=None, noregen=None, aliasresidues=None, psfgen=None, execute=True, _clean=True)#

Builds a system for CHARMM

Uses VMD and psfgen to build a system for CHARMM. Additionally it allows for ionization and adding of disulfide bridges.

Parameters:

  • mol (Molecule object) – The Molecule object containing the system

  • topo (list of str) – A list of topology rtf files. Use charmm.listFiles to get a list of available topology files. Default: [‘top/top_all36_prot.rtf’, ‘top/top_all36_lipid.rtf’, ‘top/top_water_ions.rtf’]

  • param (list of str) – A list of parameter prm files. Use charmm.listFiles to get a list of available parameter files. Default: [‘par/par_all36m_prot.prm’, ‘par/par_all36_lipid.prm’, ‘par/par_water_ions.prm’]

  • stream (list of str) – A list of stream str files containing topologies and parameters. Use charmm.listFiles to get a list of available stream files. Default: [‘str/prot/toppar_all36_prot_arg0.str’]

  • prefix (str) – The prefix for the generated pdb and psf files

  • outdir (str) – The path to the output directory Default: ‘./build’

  • caps (dict) – A dictionary with keys segids and values lists of strings describing the caps of that segment. e.g. caps[‘P’] = [‘first ACE’, ‘last CT3’] or caps[‘P’] = [‘first none’, ‘last none’]. Default: will apply ACE and CT3 caps to proteins and none caps to the rest.

  • ionize (bool) – Enable or disable ionization

  • saltconc (float) – Salt concentration (in Molar) to add to the system after neutralization.

  • saltanion ({'CLA'}) – The anion type. Please use only CHARMM ion atom names.

  • saltcation ({'SOD', 'MG', 'POT', 'CES', 'CAL', 'ZN2'}) – The cation type. Please use only CHARMM ion atom names.

  • disulfide (list of pairs of atomselection strings) – If None it will guess disulfide bonds. Otherwise provide a list pairs of atomselection strings for each pair of residues forming the disulfide bridge.

  • regenerate (None or list of strings of: ['angles', 'dihedrals']) – Disable angle/dihedral regeneration with regenerate=None, or enable it with regenerate=[‘angles’, ‘diheldrals’] or just one of the two options with regenerate=[‘angles’] or regenerate=[‘diheldrals’].

  • patches (list of str) – Any further patches the user wants to apply

  • noregen (list of str) – A list of patches that must not be regenerated (angles and dihedrals) Default: [‘FHEM’, ‘PHEM’, ‘PLOH’, ‘PLO2’, ‘PLIG’, ‘PSUL’]

  • aliasresidues (dict of aliases) – A dictionary of key: value pairs of residue names we want to alias

  • psfgen (str) – Path to psfgen executable used to build for CHARMM

  • execute (bool) – Disable building. Will only write out the input script needed by psfgen. Does not include ionization.

Returns:

molbuilt – The built system in a Molecule object

Return type:

Molecule object

Example

>>> from htmd.ui import *
>>> mol = Molecule("3PTB")
>>> mol.filter("not resname BEN")
>>> molbuilt = charmm.build(mol, outdir='/tmp/build', ionize=False)  
Bond between A: [serial 185 resid 42 resname CYS chain A segid 0]
             B: [serial 298 resid 58 resname CYS chain A segid 0]...
>>> # More complex example
>>> topos  = ['top/top_all36_prot.rtf', './BEN.rtf', 'top/top_water_ions.rtf']
>>> params = ['par/par_all36m_prot.prm', './BEN.prm', 'par/par_water_ions.prm']
>>> disu = [['segid P and resid 157', 'segid P and resid 13'], ['segid K and resid 1', 'segid K and resid 25']]
>>> ar = {'SAPI24': 'SP24'}  # Alias large resnames to a short-hand version
>>> molbuilt = charmm.build(mol, topo=topos, param=params, outdir='/tmp/build', saltconc=0.15, disulfide=disu, aliasresidues=ar)
htmd.builder.charmm.cleanup_charmm_prm(mol, parameters, outfile)#
htmd.builder.charmm.combine(prmlist, outfile)#

Combines CHARMM parameter files Take a list of parameters files and combine them into a single file (useful for acemd)

Parameters:

  • prmlist (list) – List of parameter files to combine

  • outfile (str) – Output filename of combined parameter files

htmd.builder.charmm.defaultParam()#

Returns the default parameters used by charmm.build

htmd.builder.charmm.defaultStream()#

Returns the default stream files used by charmm.build

htmd.builder.charmm.defaultTopo()#

Returns the default topologies used by charmm.build

htmd.builder.charmm.htmdCharmmHome()#

Returns the location of the CHARMM files distributed with HTMD

htmd.builder.charmm.listFiles()#

Lists all available Charmm topologies and parameter files

Examples

>>> from htmd.builder import charmm
>>> charmm.listFiles()             
---- Topologies files list...
htmd.builder.charmm.search(key, name)#

Searches for CHARMM files containing a given definition.

Parameters:

  • key (str) – A key

  • name (str) – The corresponding name

Examples

>>> charmm.search(key='RESI', name = 'CHL1')
htmd.builder.charmm.split(filename, outdir)#

Splits a stream file into an rtf and prm file.

Parameters:

filename (str) – Stream file name

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