Calculating the potential and charge density
The goal of the following APBS calculation is to generate
visualization-quality solutions to the nonlinear PBE equation and to
write out the electrostatic potential and charge density for subsequent
analysis. This procedure is carried out in the following APBS input
file, available for download
here.
Example 1. APBS DNA condensation input file
read
mol pqr dna.pqr # Read in DNA
end
elec
mg-auto
dime 97 97 161 # Rectangular grid dimensions
cglen 160 160 230 # Rectangular box
fglen 130 130 200 # Rectangular box
cgcent mol 1 # Center on the molecule
fgcent mol 1 # Center on the molecule
mol 1
npbe # Nonlinear DNA
bcfl mdh # Full multipole approximation
ion 1 0.100 2.0 # 100 mM Na+
ion -1 0.100 2.0 # 100 mM Cl-
pdie 1.0 # Solute dielectric
sdie 78.54 # Solvent dielectric
chgm spl0 # Linear charge discretization
srfm smol # Smoothed molecular surface
srad 1.4 # Solvent probe radius
swin 0.3 # Spline surface window (not used)
sdens 10.0 # Sphere density
temp 298.15 # Temperature
gamma 0.105 # Apolar coefficient
calcenergy no # No energies
calcforce no # No forces
write qdens dx qdens # Write out charge density
write pot dx pot # Write out potential
end
quit
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In this example, the full multipole boundary condition was used to
better represent the enlongated charge distribution of the DNA.
As usual, this file can then be used with APBS via the command:
where
apbs.in is the name of the downloaded
input file. This example took roughly 4 minutes on a 2.2 GHz Intel
Pentium 4.