Hello --

It appears that you've forgotten to include the "usemap" http://apbs.wustl.edu/MediaWiki/index.php/ELEC_input_file_section#usemap command in your input file.

-- Nathan

On Oct 12, 2009, at 6:15 PM, <przemekbartha@gmail.com> <przemekbartha@gmail.com> wrote:

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:
 
read 
 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
  srad 1.4
  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
 
 
 
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