1. Introduction

The Amber/APBS interface makes most of the APBS functionality available to Amber users. The APBS interface in sander is accessible through the &apbs keyword. Additionally, the igb keyword must be set to 6. This combination of keywords means that a calculation will be performed on the given system in vacuum and then APBS calculated solvation energies and forces will be added to the total energy and forces.

In addition to minimization and molecular dynamics simulation with APBS calculated implicit solvent contribution the Amber/APBS module can write out calculated electrostatic potential to a file. This file can be visualized using third party applications, including VMD, Pymol, PMV/Vision and OpenDX.

The current version of the Amber/APBS module supports serial execution only. Parallel capability will be added in later versions.

2. Installing the iAPBS Interface

2.1. Requirements

To compile iAPBS/Amber interface two packages are required:

  • APBS (version 1.5.0 or later).

  • Amber (version 16 or later)

2.2. Building iAPBS interface

Building of the iAPBS interface requires compilation and installation of MALOC and APBS libraries. The following describes all steps (assumes bash as login script, modify appropriately for t/csh). The instructions also assume working gcc/gfortran compilers. The use of Intel compilers is recomended for better performance of the compiled executables.

# create a build directory and cd to it, then:
P=`pwd`
export APBS_PREFIX=${P}
export MCSH_HOME=/dev/null

# get the source
git clone https://github.com/Electrostatics/apbs-pdb2pqr
cd apbs-pdb2pqr
git submodule init
git submodule update
mkdir apbs/build

# configure and build it
cd apbs/build
cmake -DCMAKE_INSTALL_PREFIX:PATH=${APBS_PREFIX} \
 -DCMAKE_BUILD_TYPE=Release -DBUILD_DOC=OFF \
 -DBUILD_SHARED_LIBS=OFF -DENABLE_QUIET=ON \
 -DENABLE_iAPBS=ON

make install

These steps should build the apbs executable in ${APBS_PREFIX}/bin and all the necessary apbs and iapbs libraries in ${APBS_PREFIX}/lib.

2.3. Building of Amber/APBS module

The Amber/APBS module is supported on the x86_64 Linux platform only.

# unpack your Amber and Amber Tools source code in
# ${APBS_PREFIX}/amber (or use a symlink), then:

cd $APBS_PREFIX
export AMBERHOME=${APBS_PREFIX}/amber
cd $AMBERHOME
./configure -noX11 --skip-python gnu
make install

cd ${AMBERHOME}/AmberTools/src/sander
export APBS_LIBDIR=${APBS_PREFIX}/lib
export APBS_LIBS="-liapbs -lapbs_routines -lapbs_mg -lapbs_generic -lapbs_pmgc -lmaloc -lz"
make clean
make depend
make -e AMBERBUILDFLAGS="-DAPBS" ${AMBERHOME}/bin/sander.APBS

# test it
export TESTsander=${AMBERHOME}/bin/sander.APBS
cd ${AMBERHOME}/test/iapbs_radi
./Run.ion.min

This builds the sander.APBS binary in ${APBS_PREFIX}/amber/bin.

3. Using sander.APBS

The APBS module in sander offers an alternative to the built-in PB sander module. The APBS module can be used for example for implicit solvent minimization and dynamics, calculation and visualization of miscellaneous electrostatic biomolecular properties. Please see the Examples section of this User’s Guide.

The following table lists all Amber/APBS keywords with their description. The left side of the table also lists corresponding APBS keywords which Amber/APBS keywords mimic very closely. For detailed discussion of APBS keywords please see APBS documentation.

3.1. APBS and sander.APBS keyword description

Table 1. APBS and sander.APBS input parameters
APBS Amber/APBS Description

apbs

Enters the APBS module

mg-auto/mg-para

calc_type [1]

0: manual MG; 1: autoMG; 2: parallel MG

lpbe/nbpe

nonlin [0]

Linear/full Poisson-Boltzmann equation: 0: linear; 1: non-linear; 4: size-dependent PBE

bcfl

bcfl [1]

Boundary condition method: 0: zero; 1: sdh; 2: mdh; 4: focus

srfm

srfm [2]

Surface calculation method: 0: mol; 1: smol; 2: spl2; 3: spl4

pdie

pdie [2.0]

Solute dielectric

sdie

sdie [78.4]

Solvent dielectric

sdens

sdens [10.0]

Vacc sphere density

srad

srad [1.4]

Solvent radius

swin

swin [0.3]

Cubic spline window

temp

temp [298.15]

Temperature (in K)

gamma

gamma [0.105]

Surface tension for apolar energies/forces (in kJ/mol/A2)

chgm

chgm [1]

Charge discretization method: 0: spl0; 1: spl2; 2: spl4

vol

smvolume

The parameter smvolume controls the lattice size (in Angstroms3) used in the SMPBE formalism.

size

smsize

The parameter smsize controls the relative size of the ions (in Angstroms) such that each lattice site can contain a single ion of volume radius3 or size ions of volume radius3/size.

calcenergy

calcenergy [2]

Energy calculation flag: 0: Do not perform energy calculation; 1: Calculate total energy only; 2: Calculate per-atom energy components

calcforce

calcforce [2]

Atomic forces calculation: 0: Do not perform force calculation; 1: Calculate total force only; 2: Calculate per-atom force components

write pot

wpot

Writes electrostatic potential data to iapbs-pot.dx in DX format

write charge

wchg

Writes charge data to iapbs-charge.dx in DX format

write smol

wsmol

Writes molecular surface data to iapbs-smol.dx in DX format

write kappa

wkappa

Writes the ion-accessibility kappa map to iapbs-kappa.dx in DX format

write diel

wdiel

Writes dielectric maps to iapbs-diel[x,y,z].dx in DX format

read charge

rchg

Reads charge data from iapbs-charge.dx in DX format

read kappa

rkappa

Reads the ion-accessibility kappa map from iapbs-kappa.dx in DX format

read diel

rdiel

Reads dielectric maps from iapbs-diel[x,y,z].dx in DX format

nion

Number of counterions

ionq

ionq

Counterion charges (in e)

ionc

ionc

Counterion concentrations (in M)

ionr

ionrr

Counterion radii (in A)

dime

dime

Grid dimensions (in x, y and z)

cmeth

cmeth [1]

Centering method: 0: Center on a point 1: Center on a molecule

gcent

center

Grid center if cmeth=0

ccmeth

ccmeth [1]

Coarse grid centering method: 0: Center on a point 1: Center on a molecule

cgcent

ccenter

Coarse grid center if ccmeth=0

fcmeth

fcmeth [1]

Fine grid centering method: 0: Center on a point 1: Center on a molecule

fgcent

fcenter

Fine grid center if fcmeth=0

grid

grid

Grid spacings

glen

glen

Grid side lengths

cglen

cglen

Coarse grid side lengths

fglen

fglen

Fine grid side lengths

pdime

pdime

Grid of processors to be used in calculation

ofrac

ofrac [0.1]

Overlap fraction between processors

radiopt [0]

Radii optimization: 0: use prmtop for both charge and radius; 1: read charge and radius information from pbparamsin file (format: atom_label charge radius); 2: Read charge/radius information from a PQR file; 3: Read radius information from a PQR file.

pqr

PQR file name. Used with conjuction with the radiopt option

calcnpenergy [1]

Calculate nonpolar energy [0, 1]. 0: Don’t calculate; 1: SASA-based apolar energy caclulation.

calcnpforce [2]

Calculate nonpolar forces [0, 1, 2]. 0: Do not perform force calculation; 1: Calculate total force only; 2: Calculate per-atom force components

apbs_print [1]

Verbosity of the output

apbs_debug [0]

Debugging flag

sp_apbs [.FALSE.]

Perform a single point (a single electrostatic evaluation) APBS calculation

Note
Notes
  • Values in square brackets [] are defaults. For up-to-date default values please see $AMBERHOME/src/sander/apbs.F90

  • To disable creation of io.mc file before attempting any extensive minimization or MD simulation with the APBS module please set the MCSH_HOME environment variable to /dev/null (export MCSH_HOME=/dev/null).

4. Examples of using sander.APBS

The APBS module is initialized when &apbs keyword is encountered in the input file. Also, igb must be set to 6 in the &cntrl section. The &apbs keyword can be then followed by additional apbs keywords, for details see Amber/APBS keywords.

4.1. Solvation energy calculation

This example executes a solvation energy calculation and prints out total solvation energy for the given molecule (in energy terms EPB and ENPOLAR for polar and non-polar solvation terms, respectively).

 iAPBS solvation energy example
 &cntrl
   maxcyc=0, imin=1,
   cut=12.0,
   igb=6, ntb=0,
   ntpr=1,
 /
 &apbs
    apbs_print=1
    grid=0.5, 0.5, 0.5,
    calc_type=0, cmeth=1,
    bcfl=2, srfm=1, chgm=1,
    pdie=1.0, sdie=78.54,
    srad = 1.4,
    nion=2,
    ionq  = 1.0, -1.0,
    ionc  = 0.15, 0.15,
    ionrr = 2.0, 2.0,
    radiopt = 3, pqr = 'my.pqr',
    calcforce=0, calcnpenergy=1,
 &end

4.2. Electrostatic energy calculation

This example executes a single point electrostatic energy calculation and prints out the calculated energy (in energy terms EPB and ENPOLAR for polar and non-polar terms, respectively).

 APBS electrostatic energy example
 &cntrl
   maxcyc=0, imin=1,
   cut=12.0,
   igb=6, ntb=0,
   ntpr=1,
 /
 &apbs
    apbs_print=1
    grid = 0.1, 0.5, 0.5,
    calc_type=0, cmeth=1,
    sp_apbs=.true.,
 &end

4.3. Molecular dynamics in implicit solvent using APBS

This examples shows how to use the Amber/APBS module for carrying out a molecular dynamics simulation in implicit solvent with APBS.

Example of APBS implicit solvent dynamics
&cntrl
 ntx=1, irest=0, imin=0,
 ntpr=10, ntwx=500, nscm=100, ntwr=5000,
 dt=0.001, nstlim=50,
 temp0=300, tempi=0, ntt=1, tautp=0.1,
 igb=6, cut=12.0, ntb=0,
 ntc=2, ntf=2, tol=0.000001
/
 &apbs
    apbs_print=0,
    grid = 0.5, 0.5, 0.5,
    calc_type=0,
    cmeth=1,
    bcfl=2, srfm=2, chgm=1,
    pdie=2.0, sdie=78.54,
    radiopt=2, pqr='my.pqr',
    calcforce=2, calcnpenergy=1,
    nion=2,
    ionq  = 1.0, -1.0,
    ionc  = 0.15, 0.15,
    ionrr = 2.0, 2.0,
 &end

4.4. Calculation and visualization of electrostatic potential

When this input file is run three DX files will be created. These can be visualized using several applications (for details please see APBS visualization guide). The DX files will be iapbs-pot.dx, iapbs-smol.dx and iapbs-charge.dx which will contain electrostatic potential, solvent accessible surface and charge information, respectively.

 APBS visualization example
 &cntrl
   maxcyc=0, imin=1,
   cut=12.0,
   igb=6, ntb=0
   ntpr=1,
 /
 &apbs
    apbs_print=1,
    grid= 0.5, 0.5, 0.5,
    calc_type = 0,
    srad = 0.7,
    wpot = 1, wchg = 1, wsmol =1,
    sp_apbs=.true.,
 &end
Note
Notes

To determine the correct size of the numerical grid enveloping the studied molecule (parameters cglen and fglen) you can use psize.py tool from the APBS distribution.

Parameter sp_apbs=.true. triggers only a single APBS calculation (SP, single point energy). The calculated electrostatic energy contains self-energy terms thus it is not very useful by itself. This is however useful when, for instance, generating DX files for visualization. If the parameter sp_apbs is omitted (or set to .false., which is the default) then two APBS calculations (one for a system in solvent and then in vacuum) are performed every time solvation energy and forces are recalculated. This is used during minimization and MD simulations.