Tool Set Documentation

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Latest revision as of 22:45, 13 September 2010


usage: [options] [PDBfile]
options: [-out total,bonds,angles,ureyb,dihedrals,impropers,
         [-charge] [-weight] [-volume]
         [-dipole] [-mass] [-oxyz]
         [-psf PSFfile CRDfile]
         [-mol2 MOL2file]
         [-par CHARMMparams]
         [-l min:max[=...]] [-self]
         [-log logFile] [-cmd logFile]
         [-custom file]
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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.


usage information
-out energy-terms 
specify which energy terms to output
write out all energy terms
output results in a single line
output total charge of a system
output dipole of a system
use center of mass as origin for dipole calculation (instead of center of geometry)
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
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 1vii.exp.min.pdb
evaluates the vacuum energy of a minimized structure and writes out the total energy

      -513.6242 -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