4.1. Using Amber/APBS module

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.

4.1.1. Amber/APBS Module Keywords

Table 4-1. APBS and Amber/APBS keywords

APBS keyword	Amber/APBS keyword	Description
	apbs	Enters the APBS module
mg-auto/mg-para	calc_type [0]	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 [1]	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/A^2)
chgm	chgm [1]	Charge discretization method: 0: spl0; 1: spl2; 2: spl4
vol	smvolume	The parameter smvolume controls the lattice size (in Angstroms^3) 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 radius^3 or size ions of volume radius^3/size.
calcenergy	calcenergy [1]	Energy calculation flag: 0: Do not perform energy calculation; 1: Calculate total energy only; 2: Calculate per-atom energy components
calcforce	calcforce [0]	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; 1: read charge and radius information from 'pbparamsin' file (format: atom_label charge radius); 2: Read charge/radius information for a PQR file; 3: Read radius information from a PQR file.
	pqr	PQR file name
	calcnpenergy [1]	Calculate nonpolar energy [0, 1]. 0: Don't calculate; 1: SASA-based apolar energy caclulation.
	sp_apbs [.FALSE.]	Perform SP APBS calculation

Values in square brackets [] are defaults.