Hello,

My problem, is to calculate solvation energy from a charge, placed in a center of a sphere.
The easiest way to do this, would simply be to add an ion with a certain radius in the pqr file. My goal however, is to change the shape of the sphere in the future.
As far as I understand, this requires a change in potential maps - dx files.
I generate a dx file - a space, where dielectric constant equals 80 (solvent), with a bowl, where dielectric constant equals 1 (solute). Later, I implement such map in apbs input file, together with the pqr file, so that the charge is placed in the center of the bowl.

As I run APBS calculation, everything seems to be fine.
The problem occures later: nomather how I change the shape of my solute (my dx file), the energy remains the same. It seems that APBS is not reading my maps although it says it does.

Since I am a newbie, perhaps I am missing something obvious in my calculations.

below, I include my APBS input file and the pqr file.

I would be grateful for any help
Przemek

pqr:
ATOM      1  I   ION     1       4.000   4.000  4.000  1.00  3

input file:

mol pqr ion.pqr
diel dx xBowl_65_1_80.dx yBowl_65_1_80.dx zBowl_65_1_80.dx
# diel dx xElips_33_1_80.dx yElips_33_1_80.dx zElips_33_1_80.dx
end

elec name solv           # Electrostatics calculation on the solvated state

mg-manual              # Specify the mode for APBS to run
dime 129 129 129       # The grid dimensions
nlev 4                 # Multigrid level parameter
grid 0.33 0.33 0.33    # Grid spacing
gcent mol 1            # Center the grid on molecule 1
mol 1                  # Perform the calculation on molecule 1
lpbe                   # Solve the linearized Poisson-Boltzmann
# equation
bcfl mdh               # Use all multipole moments when calculating the
# potential
pdie 1.0               # Solute dielectric
sdie 80                # Solvent dielectric
chgm spl2              # Spline-based discretization of the delta
# functions
srfm mol               # Molecular surface definition
srad 1.4               # Solvent probe radius (for molecular surface)
swin 0.3               # Solvent surface spline window (not used here)
sdens 10.0             # Sphere density of accessibility object
temp 298.15            # Temperature
gamma 0.105            # Apolar energy surface coefficient (not used here)
calcenergy total       # Calculate energies
calcforce no           # Do not calculate forces
#write pot dx potential-RADIUS
# Write out the potential
#write dielx dx mapax

end

elec name ref              # Calculate potential for reference (vacuum) state

mg-manual
dime 129 129 129
nlev 1
grid 0.33 0.33 0.33
gcent mol 1
mol 1
lpbe
bcfl mdh
pdie 1.0               # The solvent and solute dielectric constants are
# equal
sdie 1.0               # The solvent and solute dielectric constants are
# equal
chgm spl2
srfm mol
swin 0.3
sdens 10.0
temp 298.15
gamma 0.105
calcenergy total
calcforce no

#  write diely dx mapay
#  write dielz dx mapaz
#  write kappa dx kappa

end

print

energy solv - ref

end

quit