# apbs (c41b1)

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.doc

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.doc

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