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 systemtopo (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)
- 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.
Examples
>>> charmm.search(key='RESI', name = 'CHL1')