pbCHARMM.pl - Revision history

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2009-07-31T03:29:12Z

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2009-07-31T03:26:08Z

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2009-07-31T03:25:46Z

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Description

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Description

Feig at 14:13, 12 August 2006

2006-08-12T14:13:56Z

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__NOTOC__
== Usage ==

<mmtsbToolUsage cmd="pbCHARMM.pl"></mmtsbToolUsage>

== 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 &Aring. Good accuracy
at the expense of time may be obtained with 0.25 &Aring.
 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

== Examples ==

<mmtsbToolExample cmd="pbCHARMM.pl" set="/apps/mmtsb/bench/pbCHARMM.pl-test/test1"></mmtsbToolExample>

<mmtsbToolExample cmd="pbCHARMM.pl" set="/apps/mmtsb/bench/pbCHARMM.pl-test/test2"></mmtsbToolExample>

<mmtsbToolExample cmd="pbCHARMM.pl" set="/apps/mmtsb/bench/pbCHARMM.pl-test/test3"></mmtsbToolExample>

<mmtsbToolExample cmd="pbCHARMM.pl" set="/apps/mmtsb/bench/pbCHARMM.pl-test/test4"></mmtsbToolExample>

@@ Line 71: / Line 71: @@
 ; -cmd file : output CHARMM input file
 ; -custom file : provide custom CHARMM commands
-; -epsgrid file : read epsilon distribution from grid file
+; -epsgrid file : write epsilon distribution
-; -epssize num : ?
+; -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 : ?
+; -emap file :  write electrostatic potential to file
 ; -nocenter : do not center molecule before carrying out PB calculation

@@ Line 66: / Line 66: @@
 ; -threads n : parallelize calculation of atomic solvation free energies on n CPUs/cores
 ; -atomic : calculate atomic solvation free energies
-; -pairs : ?
+; -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

@@ Line 67: / Line 67: @@
 ; -atomic : calculate atomic solvation free energies
 ; -pairs : ?
-; -keepcharge : ?
+; -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

@@ Line 28: / Line 28: @@
 The grid size used in the finite difference
-solver can be changed with <B>dcel</B>. The default value is 0.5 &Aring. Good accuracy
+solver can be changed with <B>dcel</B>. The default value is 0.5 &Aring;. Good accuracy at the expense of time may be obtained with 0.25 &Aring;.
 <BR>

@@ Line 17: / Line 17: @@
 size chosen.
 <BR>
 A number of options can be given in a comma-separated list of key=value
 pairs following <B>-par</B>. The force field can be either CHARMM19 (default)
@@ Line 25: / Line 26: @@
 If the keyword <B>scalerad</B> is given, some of the radii are scaled slightly
 so that experimental solvation energies of small molecules are reproduced better.<BR>
 The grid size used in the finite difference
 solver can be changed with <B>dcel</B>. The default value is 0.5 &Aring. Good accuracy
 at the expense of time may be obtained with 0.25 &Aring.
-<BR>By default, the solvation energy is calculated for a solute with an internal dielectric
+<BR>
 of 1 transfered from vacuum (e=1) to water (e=80). The internal (solute) dielectric may be
 changed with <B>epsp</B>, the solvent dielectric with <B>epsw</B>, and the reference
@@ Line 36: / Line 40: @@
 the <B>-log</B> option. A CHARMM command file is produced if a file name is
 given with <B>-cmd</B>.<BR>
-<BR>
 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.
@@ Line 52: / Line 56: @@
 architectures. Parallelization requiring network communication
 (through MPI for example) is not supported at this point.
 == Options ==

@@ Line 59: / Line 59: @@
 ; -help : usage information
+; -par key=value[,...] : CHARMM parameters
 == Examples ==