MMTSB
Tool Set Documentation

pbCHARMM.pl

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Usage

usage:   pbCHARMM.pl [options] [PDBfile]
options: [-par param=19|22,hsd=list,hse=list,scalerad,
               smooth,dcel=value,epsp=value,epsw=value,epsr=value,
               pbionconc=value,pbtemp=value,pbionr=value]
         [-psf PSFfile CRDfile]
         [-mol2 MOL2file]
         [-radii file]
         [-partial file] [-threads n]
         [-atomic] [-pairs] [-keepcharge]
         [-log logFile] [-cmd logFile]
         [-custom file]
         [-epsgrid file] [-epssize num]
         [-grid phi|phix|chrg|epsx|epsy|epsz file] [-dx]
         [-emap file]
         [-nocenter]
Show source


Description

This script uses the PBEQ module in CHARMM to evaluate the electrostatic contribution of the solvation free energy by solving the Poisson-Boltzmann equation. It expects a protein structure in PDB format either from a file given as the last command line argument or passed through standard input. Alternatively, CHARMM PSF and coordinate files can be given with -psf in order to provide the input structure. The calculated energy value is written to standard output. Please note that solving the Poisson-Boltzmann equation may be time-demanding and can take from minutes to hours depending on the size of the molecule and the grid size chosen.

A number of options can be given in a comma-separated list of key=value pairs following -par. The force field can be either CHARMM19 (default) or CHARMM22 and is selected with param=19 or param=22, respectively. Protonation sites for histidine residues may be specified explicitly by providing the corresponding residue number(s) with hsd (protonated at ND1) or hse (protonated at NE2). If the keyword scalerad is given, some of the radii are scaled slightly so that experimental solvation energies of small molecules are reproduced better.

The grid size used in the finite difference solver can be changed with dcel. The default value is 0.5 Å. Good accuracy at the expense of time may be obtained with 0.25 Å.

By default, the solvation energy is calculated for a solute with an internal dielectric of 1 transfered from vacuum (e=1) to water (e=80). The internal (solute) dielectric may be changed with epsp, the solvent dielectric with epsw, and the reference dielectric (vacuum by default) with epsr.

The output from CHARMM can be saved in a file with the -log option. A CHARMM command file is produced if a file name is given with -cmd.

This script can also be used to calculate standard solvation free energies for a single charged atom in the context of an otherwise uncharged solute. This option is selected with -atomic. By default a unity charge is assumed, but the option -keepcharge can be given to use the force field charge instead. It is also possible to calculate solvation free energies for all pairs of charged atoms with -pairs in a similar fashion. Please be advised that the number of pairs even for small systems becomes quite large and will require significant time for the Poisson-Boltzmann calculations to complete. The output contains the Poisson-Boltzmann energy for each atom as well as the corresponding Generalized Born radius calculated as -166.0/Epb. Only in this mode the calculation can be distributed over a number of threads given with -threads if more than one CPU is available. This form of parallelization works only on SMP (shared memory) architectures. Parallelization requiring network communication (through MPI for example) is not supported at this point.

Options

-help 
usage information
-par key=value[,...] 
CHARMM parameters
-psf PSFfile CRDfile 
read topology and initial conformation from CHARMM PSF and CRD files
-mol2 MOL2file 
read topology and initial conformation from MOL2 file
-radii file 
read modified van der Waals radii from external file
-partial file 
 ?
-threads n 
parallelize calculation of atomic solvation free energies on n CPUs/cores
-atomic 
calculate atomic solvation free energies
-pairs 
calculate solvation free energies for pairs of atoms
-keepcharge 
use force field charge instead of unit charge when calculating atomic solvation free energies
-log file 
output CHARMM log file
-cmd file 
output CHARMM input file
-custom file 
provide custom CHARMM commands
-epsgrid file 
write epsilon distribution
-epssize num 
size of epsilon grid to be written out
-grid phi|phix|chrg|epsx|epsy|epsz file 
write grid file
-dx 
write grid file in DX format
-emap file 
write electrostatic potential to file
-nocenter 
do not center molecule before carrying out PB calculation

Examples

pbCHARMM.pl 1vii.exp.min.pdb
calculates the Poisson-Boltzmann electrostatic solvation free energy

-553.329900


pbCHARMM.pl -par dcel=0.4 -log charmm.log 1vii.exp.min.pdb
calculates the Poisson-Boltzmann electrostatic solvation free energy using a (smaller) grid size of 0.4 A. The CHARMM output is written to charmm.log.

-504.321230


pbCHARMM.pl -par dcel=0.75 -atomic -threads 2 1vii.exp.min.pdb
calculates the standard atomic electrostatic solvation free energies for all atoms in the given PDB structure. A grid cell size of 0.75 A and two threads are used to speed up the calculation.

:1:HT1:1 -151.666690 1.081057
:1:HT2:2 -74.058550 2.213929
:1:N:3 -70.039090 2.340983
:1:HT3:4 -109.583070 1.496220
:1:CA:5 -56.644740 2.894538
:1:CB:6 -60.355740 2.716566
:1:CG:7 -64.488680 2.542467
:1:SD:8 -72.487170 2.261922
:1:CE:9 -74.914680 2.188628
:1:C:10 -57.106690 2.871123

...


pbCHARMM.pl -par dcel=0.4,epsp=2,epsw=40 1vii.exp.min.pdb
calculates the transfer energy from vacuum to a medium with a dielectric constant of 40. Also, an internal solute dielectric of 2 is used instead of 1.

-379.108250