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setEnergyLogFile(file) |
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sets an energy log file and switches on energy logging
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setPertLogFile(file) |
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sets an pert log file
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logEnergy(tag) |
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writes the energy output from the last energy evaluation or minimization run to the energy log file if one has been set before with setEnergyLogFile. A tag is required to provide identification of the output in the log file.
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logMDEnergy(tag) |
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writes energy output from the last dynamics run to the energy log file if one has been set before. A tag is required as in logEnergy.
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logPertOutput() |
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writes pert output to the pert log file if one has been set before.
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finish() |
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stops CHARMM and closes the connection and all log files. After this function has been called CHARMM commands can no longer be used. It is called automatically by the package destructor if it has not called explicitly.
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closeEnergy() |
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closes the energy log file
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loadParameters([parameters]) |
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CHARMM load topology and parameter files into CHARMM. This should be called as one of the first CHARMM commands before any structures are loaded. Depending on the parameter param CHARMM19 or CHARMM22 parameters are loaded. The parameter may be set through a hash-type key=>value pair argument.
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clearEnergy([parameters]) |
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clears energy components
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setupEnergy([parameters]) |
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setups all energy components
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setupFromMol2(mol2file) |
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reads in a MOL2 file to setup structure
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setupFromPSF(psffile,crdfile) |
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reads in a PSF structure and reads coordinates from a CHARMM coordinate file
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setupFromPDB(pdbfile[,terminalgroup]) |
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generates the CHARMM PSF structure from a protein structure in a PDB file. It also rebuilds missing atoms and adds hydrogens, if necessary. The type of terminal groups may be selected through the second argument. Possible options are none, ends, and all.
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setupFromMolecule(mol[,terminalgroup]) |
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generates the CHARMM PSF structure from a protein structure in a Molecule object.
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readFromPDB(pdbfile) |
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reads coordinates for a protein structure from a PDB file if the PSF was setup before with setupFromMolecule. This is useful for repeating a modeling procedure for different conformations of the same protein. As setupFromMolecule this method also rebuilds missing atoms and adds hydrogens if necessary.
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readFromPDB(pdbfile) |
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reads coordinates for a protein structure from a PDB file if the PSF was setup before with setupFromMolecule. This is useful for repeating a modeling procedure for different conformations of the same protein. As setupFromMolecule this method also rebuilds missing atoms and adds hydrogens if necessary.
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loadReference(molecule) |
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reads coordinates for a protein structure from a PDB file into the alternate COMP coordinate set
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initCoordinates() |
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initializes all coordinates
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setupNonBonded([parameters]) |
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calls the CHARMM command update to set non-bonded interaction parameters. Options are constant (dielec=>"CDIE") or distance-dependent dielectric (dielec=>"RDIE"), the dieletric constant epsilon and interaction and list cutoffs (cutnb, cuton, cutoff). Force shifting is set for electrostatics as well as van der Waals interactions as the default for vacuum minimizations.
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setupEEF1([parameters]) |
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sets up EEF1
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setupHBond([parameters]) |
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sets up hydrogen bonding list
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setupOG([parameters]) |
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sets up Olgun's scoring function
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setupACE([parameters]) |
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sets up ACE
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setupASP([parameters]) |
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sets up atomic solvation parameter based energy function
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clearASP() |
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switch off ASP energy terms
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_scaleRadii(name) |
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scales radii for GB/PB
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setupGB([parameters]) |
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sets up the Generalized Born solvent approximation The non-bonded interactions are set to constant dielectric, epsilon = 1.0, and force switching. GB is then initialized and will be used in all subsequent energy evaluations.
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clearGB() |
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clear and switch off Generalized Born solvent approximation
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noeRestraints([parameters]) |
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sets up NOE restraints with CHARMM input from file in noe parameter
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getNOEAnalysis() |
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obtain NOE distance restraint violations from CHARMM
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minimizeSD([parameters]) |
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runs a steepest descent minimization. Parameters are the non-bonded list update frequency updnbsd, the number of minimization steps itersd and the initial step size stepsd.
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minimize([parameters]) |
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runs minimization protocol Parameters are the non-bonded list update frequency minupdnb, the number of minimization steps miniter, the initial step size minstep and an energy tolerance minetol to limit the minimization run if the tolerance is reached in less than the requested number of runs. The minimization algorithm can be changed by setting minmode.
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shake([parameters]) |
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turns on SHAKE to fix bond distances. A fast mode is available if the parameter shakefast is set. All bonds, including hydrogens, are fixed if shakemode is set to hyd, otherwise bonds involving hydrogens are excluded. The SHAKE tolerance is determined by shaketol.
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periodicBoundaries([parameters]) |
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turns on periodic boundaries.
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ewald([parameters]) |
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turns on Ewald summation (PME) for non-bonded electrostatics. The parameters pmekappa is used to set the kappa value.
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setupPHMD([parameters]) |
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set up PHMD simulation parameters are defined in phmd.doc
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runDynamics(restin,restout,trajout,enerout[,parameters]) |
|
runs a molecular dynamics simulation. The first four arguments are file names for restart input and output, trajectory output and CHARMM energy output files. undef can be used instead of a file name if the corresponding file should not be created. If undef is given for the restart input file, the simulation is started with a random velocity assignment. A large number of parameters are available to control the simulation run. The most important values are dynsteps (number of dynamics steps), dyntemp (temperature), dynens (ensemble: "NVT" or "NPT"), dynoutfrq (frequency of energy output), dyneqfrq (frequency of velocity reassignment to maintain constant temperature in NVT), and dynpress (pressure for NPT ensemble).
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setupChargeFEP(select) |
|
setup PERT
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| |
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runPertWHAM(filename) |
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| |
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runChargeFEP(trajout,wham,pertfile[,parameters]) |
|
runs PERT to obtain charging free energy
|
| |
|
setupRestraints(fscale,conslist) |
|
sets up harmonic restraints from a list of cons data structures (see harmonicRestraint). The first argument determines the scaling factor for all force constants.
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| |
|
harmonicRestraint(cons[,fscale[,keep]]) |
|
sets up harmonic restraints according to the cons argument. It is expected to have the following data structure: cons -> {type, list[] -> {from, to, force}, sel}. The type field is either self (current coordinates) or ref (alternate coordinates in COMP). list contains a list of protein segments that are supposed to be restrained. sel identifies which atoms are restrained for each residue in the selection list (ca, cb, cab, heavy, or all). An additional argument may be given to scale all restraint forces by a factor. If the last argument is set to 1 previously set reference coordinates will be used and only force constants are updated.
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| |
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simpleRestraint(force,select,keep,comp) |
|
requests harmonic restraints with a simpler interface as harmonicRestraint. The arguments are a force constant, a CHARMM selection expression and flags whether to keep previous coordinates and whether to use coordinates from the alternate coordinate set
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| |
|
hmcmRestraint(cons[,fscale]) |
|
sets up harmonic center of mass restraints according to side chain centers from a SICHO chain file given in the reffile field of the cons argument.
|
| |
|
clearRestraints() |
|
clears all harmonic restraints
|
| |
|
applyBias(parameters) |
|
imposes a harmonic restraint of the type described in the biastype data structure. This data structure must contain the key "type", while other type-dependent keys may also be present.
|
| |
|
clearBias(parameters) |
|
clear the harmonic restraint of the type described in the biastype data structure.
|
| |
|
val = getBiasVal(parameters) |
|
return the current value of the variable to which the restraint was applied
|
| |
|
getEntropy() |
|
carries out normal mode analysis to get vibrational entropy translational and rotational entropies are also calculated and returned
|
| |
|
quasiHarmonicAnalysis(dcdfile,modes) |
|
carries out quasi harmonic analysis within CHARMM
|
| |
|
normalModeAnalysis(modes,block) |
|
carries out normal mode analysis within CHARMM specifies the number of modes if set to 1 requests block normal mode analysis
|
| |
|
nmaICSample(modefile,scale,scalepar) |
|
extrapolates coordinates along internal coordinate normal mode
|
| |
|
verbose(command) |
|
runs an arbitrary CHARMM command. Please note, that for commands requiring multiple lines all lines have to be given at once as a single argument.
|
| |
|
stream(command) |
|
sends multiple command lines to CHARMM. It returns only after the last command is finished
|
| |
|
writePDB(file) |
|
has CHARMM write out the current coordinates to a file in PDB format.
|
| |
|
writePSF(file) |
|
|
| |
|
writeCRD(file) |
|
has CHARMM write out the current coordinates to a file in CRD format.
|
| |
|
orient() |
|
orients the current structure centered at the origin and with the principal moments of inertia aligned with the principal axes.
|
| |
|
$stat = coorStats() |
|
gets coordinate statistics for the current structure and returns a data structure with the following elements: atoms (number of atoms), xmin, xmax, xcenter, ymin, ymax, ycenter, zmin, zmax, zcenter (cartesian dimensions).
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| |
|
$energy = poissonBoltzmann() |
|
calculates the non-hydrophobic contribution to the solvation free energy by solving the Poisson-Boltzmann equation. The only argument is the grid size used for the finite difference solution grid.
|
| |
|
pbgrid(gridfile,name) |
|
generates the molecular surface with PBEQ and writes the surface into a grid file
|
| |
|
epsgrid(gridfile,max) |
|
generates the molecular surface with PBEQ and writes the surface into a grid file
|
| |
|
$energy = atomPoissonBoltzmann(index) |
|
calculates the Poisson-Boltzmann energy for a single atom with unity charge while all other charges are set to zero The atom index and the finite difference solution grid size are required as arguments. Please note: This command does not restore the original charges from the force field.
|
| |
|
$list = getScalar(name[,selection]) |
|
obtains the list of values for a scalar quantity in CHARMM.
|
| |
|
value=getDipole() |
|
obtain molecular dipole
|
| |
|
value=getTotalCharge() |
|
obtain total charge of system
|
| |
|
$val = reportVariable(name) |
|
returns the value of a CHARMM ?variable.
|
| |
|
solvAccessSurf([accu[,rprobe]]) |
|
calculates the solvent accessible surface area. A desired accuracy and probe radius may be given as argument.
|
| |
|
$sasa = getSASAOutput() |
|
extracts solvent accessible surface area output after solvAccessSurf has been called and returns a data structure with the surface area in area and the associated hydrophobic contribution to the free energy of solvation in energy
|
| |
|
logSASA() |
|
writes out solvent accessible surface area and the hydrophobic contribution to the solvation free energy to the energy log file after solvAccessSurf has been called.
|
| |
|
$ener = getEnergy() |
|
evaluates the energy of the current conformation and returns a data structure with the energy components
|
| |
|
$rg = getRg() |
|
evaluates and returns the radius of gyration of the current conformation
|
| |
|
$rmsd = getRMSD() |
|
evaluates and returns the RMSD with respect to the structure in COMP
|
| |
|
$rho = getRho() |
|
evaluates and returns the "continuous" fraction of native contacts of the current conformation
|
| |
|
boxsizeFromRestart() |
|
extract boxsize from restart file
|
