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
ATOM 1 I ION 1 4.000 4.000 4.000 1.00 3
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
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
bcfl mdh # Use all multipole moments when calculating the
pdie 1.0 # Solute dielectric
sdie 80 # Solvent dielectric
chgm spl2 # Spline-based discretization of the delta
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
elec name ref # Calculate potential for reference (vacuum) state
dime 129 129 129
grid 0.33 0.33 0.33
gcent mol 1
pdie 1.0 # The solvent and solute dielectric constants are
sdie 1.0 # The solvent and solute dielectric constants are
# write diely dx mapay
# write dielz dx mapaz
# write kappa dx kappa
energy solv - ref
is the only developer event you need to attend this year. Jumpstart your
ahead of the curve. Join us from November 9 - 12, 2009. Register now!