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enerCHARMM.pl
Usage
usage: enerCHARMM.pl [options] [PDBfile]
options: [-out total,bonds,angles,ureyb,dihedrals,impropers,
vdwaals,elec,gb,sasa,asp]
[-all]
[-oneline]
[-noout]
[-charge] [-weight] [-volume]
[-dipole] [-mass] [-oxyz]
[-psf PSFfile CRDfile]
[-mol2 MOL2file]
[-par CHARMMparams]
[-l min:max[=...]] [-self]
[-log logFile] [-cmd logFile]
[-custom file]
Description
This script uses CHARMM to evaluate the energy of a protein structure from a PDB file
or from a CHARMM PSF and coordinate files given with -psf.
It does not perform any minimization or refinement and is most useful with previously
minimized structures. A common application is the evaluation of implicit solvent
Generalized Born energy terms for structures that have been minimized in vacuum only
as a compromise between speed and accuracy of the energy score.
CHARMM parameters can be given in a list of key=value pairs with -par. A
list of all available parameters is given
here.
Once the energies have been evaluated the total energy or some or all components may be
written to standard output. The flag -out is used to specify a list of desired
energy values, separated by commas.
Possible choices are total, bonds, angles,
ureyb, dihedrals, impropers, vdwaals, elec,
gb, and sasa (hydrophobic solvation free energy based on solvent
accessible surface). All available energy values are written out with -all.
It is also possible to specify limited arithmetic operators. + and - are supported
to report a sum or difference, a multiplicative factor can be given with *
in front of a property name. If more than one value is requested they are
reported each on a separate line. The flag -oneline can be used to request
that multiple values are written out in a single line, separated by spaces.
By default only the total energy is written out.
Rather than the total energy it is also possible to calculate interaction energies
for a subset of residues with this utility. To do this the residue range
of interest has to be given with -l. Then, the interaction energy of those
residues with themselves and with all other residues are calculated.
If the option -self is given only the self energy contributions are considered.
The option -log is available to save the complete
output from CHARMM under the given file name. Commands sent to CHARMM are saved in
a file with -cmd.
The location of the CHARMM binary and data directory are
set from the environment variables CHARMMEXEC and CHARMMDATA or
deduced from a charmm binary found in the search path.
Options
- -help
- usage information
- -out energy-terms
- specify which energy terms to output
- -all
- write out all energy terms
- -oneline
- output results in a single line
- -charge
- output total charge of a system
- -dipole
- output dipole of a system
- -mass
- use center of mass as origin for dipole calculation (instead of center of geometry)
- -oxyz
- use origin of coordinate system as origin for dipole calculation
- -psf PSFfile CRDfile
- load topology and coordinates from PSF and CRD files
- -mol2 MOL2file
- load topology and coordinates from MOL2 file
- -par key=value[,...]
- CHARMM parameter
- -l min:max[=...]
- calculate interaction energies of residue range with itself and rest of system
- -self
- only output self energies for residue range
- -log file
- CHARMM log file
- -cmd file
- CHARMM input file
- -custom file
- CHARMM custom file loaded before energy calculation
Examples
enerCHARMM.pl 1vii.exp.min.pdb
evaluates the vacuum energy of a minimized structure and writes out the total energy
-513.6242
enerCHARMM.pl -out total,elec,gb,sasa,gb+sasa -par param=19,gb,nocut -log charmm.log 1vii.exp.min.pdb
evaluates the energy of a minimized structure with the CHARMM19 force field without any cutoffs including
Generalized Born implicit solvent approximation. The output consists of the total energy as well
as the electrostatic energy, Generalized Born energy, hydrophobic solvation energy, and the
total solvation free energy as the sum of both the GB and hydrophobic terms.
The CHARMM output is saved in charmm.log.
total -2546.4876 elec -1844.9636 gb -527.2209 sasa 16.4835 gb+sasa -510.7373