apbs (c49b1)
Adaptive Poisson-Boltzmann Solver (APBS)
The APBS module integrates APBS (Adaptive Poisson-Boltzmann
Solver, http://www.poissonboltzmann.org/apbs) with CHARMM. For detailed
documentation and implementation information please see the official
iAPBS web site http://mccammon.ucsd.edu/iapbs
Please send any comments or bug reports to Robert Konecny (rok@ucsd.edu).
* Syntax | Syntax of the PBEQ commands
* Function | Purpose of each of the commands
* Examples | Usage examples of the PBEQ module
The APBS module integrates APBS (Adaptive Poisson-Boltzmann
Solver, http://www.poissonboltzmann.org/apbs) with CHARMM. For detailed
documentation and implementation information please see the official
iAPBS web site http://mccammon.ucsd.edu/iapbs
Please send any comments or bug reports to Robert Konecny (rok@ucsd.edu).
* Syntax | Syntax of the PBEQ commands
* Function | Purpose of each of the commands
* Examples | Usage examples of the PBEQ module
Top
Description
-----------
APBS (Adaptive Poisson-Boltzmann Solver) is a software package for the
numerical solution of the Poisson-Boltzmann equation (PBE), one of the
most popular continuum models for describing electrostatic
interactions between molecular solutes in salty, aqueous media. APBS
was designed to efficiently evaluate electrostatic properties for a
wide range of length scales to enable the investigation of molecules
with tens to millions of atoms.
The APBS/CHARMM module makes most of APBS functionality available from
within CHARMM. This allows to perform variety of calculations which
includes: evaluation of electrostatic properties of biomolecular
systems, performing optimization and molecular dynamics in implicit
solvent using APBS calculated solvation forces, visualization of
calculated electrostatic properties, etc.
Since this module's functionality overlaps in many aspects
functionality of the CHARMM's PBEQ module please read also pbeq.info
file and example input files.
Description
-----------
APBS (Adaptive Poisson-Boltzmann Solver) is a software package for the
numerical solution of the Poisson-Boltzmann equation (PBE), one of the
most popular continuum models for describing electrostatic
interactions between molecular solutes in salty, aqueous media. APBS
was designed to efficiently evaluate electrostatic properties for a
wide range of length scales to enable the investigation of molecules
with tens to millions of atoms.
The APBS/CHARMM module makes most of APBS functionality available from
within CHARMM. This allows to perform variety of calculations which
includes: evaluation of electrostatic properties of biomolecular
systems, performing optimization and molecular dynamics in implicit
solvent using APBS calculated solvation forces, visualization of
calculated electrostatic properties, etc.
Since this module's functionality overlaps in many aspects
functionality of the CHARMM's PBEQ module please read also pbeq.info
file and example input files.
Top
Syntax
------
The APBS/CHARMM module mimics APBS syntax as close as possible. For
detailed description and discussion of all APBS parameters please see
APBS documentation (http://www.poissonboltzmann.org/apbs/user-guide) and
APBS/CHARMM documentation
(http://mccammon.ucsd.edu/iapbs/usersguide/index.html) for specific
instructions for using APBS inside of CHARMM.
Syntax
------
The APBS/CHARMM module mimics APBS syntax as close as possible. For
detailed description and discussion of all APBS parameters please see
APBS documentation (http://www.poissonboltzmann.org/apbs/user-guide) and
APBS/CHARMM documentation
(http://mccammon.ucsd.edu/iapbs/usersguide/index.html) for specific
instructions for using APBS inside of CHARMM.
Top
Installation
------------
For complete installation instructions please see
http://mccammon.ucsd.edu/iapbs/usersguide/index.html
In summary:
1. first download and install the following packages: atlas (BLAS),
maloc, apbs and iapbs
2. set the following environment variables APBS_LIB, IAPBS_LIB,
APBS_BLAS:
APBS_LIB - points to where libapbs.a and libmaloc.a are installed
IAPBS_LIB - points to where libiapbs.a is installed
APBS_BLAS "-L${BLAS_LIB} -llapack -lcblas -lf77blas -latlas"
where BLAS_LIB is a directory where BLAS library is
located; these flags are BLAS-dependent, the above
example works with ATLAS
3. run 'install.com gnu medium APBS' to compile APBS-enabled CHARMM
Installation
------------
For complete installation instructions please see
http://mccammon.ucsd.edu/iapbs/usersguide/index.html
In summary:
1. first download and install the following packages: atlas (BLAS),
maloc, apbs and iapbs
2. set the following environment variables APBS_LIB, IAPBS_LIB,
APBS_BLAS:
APBS_LIB - points to where libapbs.a and libmaloc.a are installed
IAPBS_LIB - points to where libiapbs.a is installed
APBS_BLAS "-L${BLAS_LIB} -llapack -lcblas -lf77blas -latlas"
where BLAS_LIB is a directory where BLAS library is
located; these flags are BLAS-dependent, the above
example works with ATLAS
3. run 'install.com gnu medium APBS' to compile APBS-enabled CHARMM
Top
Examples
--------
There are three example input files provided with this release:
Example (1)
- Simple calculation of electrostatic energies (apbs_elstat.inp)
This shows how to do a single point electrostatic evaluation on a
molecule. The result is electrostatic energy of the molecule.
PBEQ
stream @0radius.str
APBS mgauto lpbe dimx 65 dimy 65 dimz 65 -
cglx 30 cgly 30 cglz 30 fglx 15 fgly 15 fglz 15 -
srfm 2 -
calcene 1 -
sele all END
set elstaten80 = ?enpb
APBS mgauto lpbe dimx 65 dimy 65 dimz 65 -
cglx 30 cgly 30 cglz 30 fglx 15 fgly 15 fglz 15 -
srfm 2 sdie 1.0 -
calcene 1 -
sele all END
set elstaten1 = ?enpb
END
! Electrostatic free energy of solvation
calc solv = @elstaten80 - @elstaten1
Example (2)
- Molecular dynamics in implicit solvent (apbs_md.inp)
This is an example of a short molecular dynamics simulation in
implicit solvent using APBS-calculated solvation forces.
PBEQ
set factor 0.939
set sw 0.4
stream @0radius.str
scalar wmain add @sw
scalar wmain mult @factor
scalar wmain set 0.0 sele type H* end
APBS mgauto lpbe dimx 65 dimy 65 dimz 65 -
cglx 30 cgly 30 cglz 30 fglx 15 fgly 15 fglz 15 -
swin @sw srfm 2 -
calcene 1 calcfor 1 -
sforce -
sele all END
END
skip none
dynamics leap verlet strt nstep 20 timestep 0.001 -
firstt 100.0 finalt 300.0 teminc 100.0 -
twindh 10.0
Example (3)
- Visualization of calculated elstat properties (apbs_vis.inp)
This input file show how to generate properties files (electrostatics,
SASA and charge) which can be then visualized using an external
application (VMD, PyMol, OpenDX, etc; for details please see the APBS
Examples at http://www.poissonboltzmann.org/apbs/examples).
PBEQ
stream @0radius.str
APBS mgauto lpbe dimx 65 dimy 65 dimz 65 -
cglx 30 cgly 30 cglz 30 fglx 15 fgly 15 fglz 15 -
calcene 1 -
ionq1 1.0 ionc1 0.15 ionr1 2.0 ionq2 -1.0 ionc2 0.15 ionr2 2.0 -
wpot wsmol wchg -
sele all END
END
Examples
--------
There are three example input files provided with this release:
Example (1)
- Simple calculation of electrostatic energies (apbs_elstat.inp)
This shows how to do a single point electrostatic evaluation on a
molecule. The result is electrostatic energy of the molecule.
PBEQ
stream @0radius.str
APBS mgauto lpbe dimx 65 dimy 65 dimz 65 -
cglx 30 cgly 30 cglz 30 fglx 15 fgly 15 fglz 15 -
srfm 2 -
calcene 1 -
sele all END
set elstaten80 = ?enpb
APBS mgauto lpbe dimx 65 dimy 65 dimz 65 -
cglx 30 cgly 30 cglz 30 fglx 15 fgly 15 fglz 15 -
srfm 2 sdie 1.0 -
calcene 1 -
sele all END
set elstaten1 = ?enpb
END
! Electrostatic free energy of solvation
calc solv = @elstaten80 - @elstaten1
Example (2)
- Molecular dynamics in implicit solvent (apbs_md.inp)
This is an example of a short molecular dynamics simulation in
implicit solvent using APBS-calculated solvation forces.
PBEQ
set factor 0.939
set sw 0.4
stream @0radius.str
scalar wmain add @sw
scalar wmain mult @factor
scalar wmain set 0.0 sele type H* end
APBS mgauto lpbe dimx 65 dimy 65 dimz 65 -
cglx 30 cgly 30 cglz 30 fglx 15 fgly 15 fglz 15 -
swin @sw srfm 2 -
calcene 1 calcfor 1 -
sforce -
sele all END
END
skip none
dynamics leap verlet strt nstep 20 timestep 0.001 -
firstt 100.0 finalt 300.0 teminc 100.0 -
twindh 10.0
Example (3)
- Visualization of calculated elstat properties (apbs_vis.inp)
This input file show how to generate properties files (electrostatics,
SASA and charge) which can be then visualized using an external
application (VMD, PyMol, OpenDX, etc; for details please see the APBS
Examples at http://www.poissonboltzmann.org/apbs/examples).
PBEQ
stream @0radius.str
APBS mgauto lpbe dimx 65 dimy 65 dimz 65 -
cglx 30 cgly 30 cglz 30 fglx 15 fgly 15 fglz 15 -
calcene 1 -
ionq1 1.0 ionc1 0.15 ionr1 2.0 ionq2 -1.0 ionc2 0.15 ionr2 2.0 -
wpot wsmol wchg -
sele all END
END