Input Keywords for Polar Solvation Energy

polar

polar          = yes

This will allow the calculation of polar solvation energy. The value can change to “no” if one doesn’t want to do polar calculation.

cfac

cfac           = 2

The factor by which molecular dimensions should expand to get a coarse grid dimensions. For detail see help of a APBS script apbs-1.3-source/tools/manip/psize.py (psize.py -h).

fadd

fadd           = 20

The amount (in Å) to add to molecular dimensions to get a fine grid dimensions. For detail see help of a APBS script apbs-1.3-source/tools/manip/psize.py (psize.py -h).

gridspace

gridspace      = 0.2

It specifies the value (in Å) for fine grid spacing. For detail see help of a APBS script apbs-1.3-source/tools/manip/psize.py (psize.py -h).

gmemceil

gmemceil       = 4000

Usage: Sets memory (in MB) which will be used per-processor for a calculation. For detail see help of a APBS script apbs-1.3-source/tools/manip/psize.py (psize.py -h).

PBsolver

PBsolver        = npbe

This specifies whether linear or nonlinear Poisson Boltzmann equation should be solved. The accepted keywords are lpbe and npbe for linear and traditional non-linear PB equation, respectively. The effects of different value on the polar calculation is checked during this implementation.

mg-type

mg-type        = mg-auto

How multigrid PB calculation should be performed? Accepted keywords: mg-auto and mg-para.

Note

pcharge

pcharge        = 1

The charge of positive ions in bulk solution.

prad

prad           = 0.95

Radius of positive ions.

pconc

pconc          = 0.150

Concentration of positive ion.

ncharge

ncharge        = -1

The charge of negative ions in bulk solution.

nrad

nrad           = 1.81

Radius of negative ion.

nconc

nconc = 0.150

Concentration of negative ion.

pdie

pdie           = 4

The value of solute dielectric constant. This can be change depending on the solute used for calculation. For highly charged solute high dielectric value will produce more accurate polar solvation energy.

sdie

sdie           = 80

The value of solvent dielectric constant.

vdie

vdie           = 1

The value of vacuum dielectric constant.

srad

srad           = 1.4

This specify the radius (in Å) of solvent molecules. This is used in case of probe-based surface definition.

Note

More details can be found on APBS documentation.

swin

swin           = 0.30

This specify the value for cubic spline window for spline-based surface definitions. Not used when probe-based surface are used in calculation.

Note

More details can be found on APBS documentation.

srfm

srfm           = smol

This specify the model used to construct the dielectric and ion-accessibility coefficients. The accepted keywords are mol, smol, spl2 and spl4 and it may affect the polar energy calculation.

Note

More details can be found on APBS documentation.

sdens

sdens          = 10

Specify the number of grid points per \(\text{Å}^2\) for constructing the molecular surface or solvent accessible surface. Not taken in consideration when srad = 0.0 or srfm = spl2.

Note

More details can be found on APBS documentation.

temp

temp           = 300

This specify the temperature used for Poisson-Boltzmann calculation.

Note

More details can be found on APBS documentation.

chgm

chgm            = spl4

This specify the method used to map the biomolecular point charges to the grid for a multigrid Poisson-Boltzmann calculation. The accepted keywords are spl0, spl2 and spl4. The effects of these keywords on energy are not tested in this implementation.

Note

More details can be found on APBS documentation.

bcfl

bcfl            = mdh

It specifies the type of boundary conditions used to solve the Poisson-Boltzmann equation. The accepted keywords are zero, sdh, mdh, focus, and map. However, use of focus, and map will terminate g_mmpbsa with error. The change in bcfl keywords may affect the polar energy calculation. The effects of these keywords on energy are not tested in this implementation.

Note

More details can be found on APBS documentation.