#
# Note that most of the comments here were taken from sample
# input files that came with APBS.  You can find APBS at
# http://agave.wustl.edu/apbs/
# Note that APBS is GPL'd code.
#
read
    mol pqr /net/lutefisk/slars/groel_md/1XCK/analysis/24_browdye/trans.pqr       # read molecule 1
end
elec
    mg-auto
    dime   353 193 353  # number of find grid points
                     # calculated by psize.py
    cglen   253.798100 137.535100 252.832500 # coarse mesh lengths (A)
    fglen   169.293000 100.903000 168.725000 # fine mesh lengths (A)
                     # calculated by psize.py
    cgcent 2.975500 8.259500 13.450500  # (could also give (x,y,z) form psize.py) #known center
    fgcent 2.975500 8.259500 13.450500  # (could also give (x,y,z) form psize.py) #known center
    lpbe               # solve the full nonlinear PBE with npbe
    #lpbe            # solve the linear PBE with lpbe
    bcfl sdh          # Boundary condition flag
                     #  0 => Zero
                     #  1 => Single DH sphere
                     #  2 => Multiple DH spheres
                     #  4 => Focusing
                     #
    #ion 1 0.000 2.0 # Counterion declaration:
    ion charge  1 conc 0.150000 radius 2.000000     # Counterion declaration:
    ion charge -1 conc 0.150000 radius 1.800000     # ion <charge> <conc (M)> <radius>
    ion charge  2 conc 0.000000 radius 2.000000     # ion <charge> <conc (M)> <radius>
    ion charge -2 conc 0.000000 radius 2.000000     # ion <charge> <conc (M)> <radius>
    pdie 2.000000          # Solute dielectric
    sdie 78.000000          # Solvent dielectric
    chgm spl2          # Charge disc method
                     # 0 is linear splines
                     # 1 is cubic b-splines
    mol 1            # which molecule to use
    srfm smol        # Surface calculation method
                     #  0 => Mol surface for epsilon;
                     #       inflated VdW for kappa; no
                     #       smoothing
                     #  1 => As 0 with harmoinc average
                     #       smoothing
                     #  2 => Cubic spline 
    srad 1.400000          # Solvent radius (1.4 for water)
    swin 0.3         # Surface cubic spline window .. default 0.3
    temp 310.000000          # System temperature (298.15 default)
    sdens 10.000000         # Specify the number of grid points per square-angstrom to use in Vacc object. Ignored when srad is 0.0 (see srad) or srfm is spl2 (see srfm). There is a direct correlation between the value used for the Vacc sphere density, the accuracy of the Vacc object, and the APBS calculation time. APBS default value is 10.0.
    #gamma 0.105      # Surface tension parameter for apolar forces (in kJ/mol/A^2)
                     # only used for force calculations, so we don't care, but
                     # it *used to be* always required, and 0.105 is the default
    calcenergy no    # Energy I/O to stdout
                     #  0 => don't write out energy
                     #  1 => write out total energy
                     #  2 => write out total energy and all
                     #       components
    calcforce no     # Atomic forces I/O (to stdout)
                     #  0 => don't write out forces
                     #  1 => write out net forces on molecule
                     #  2 => write out atom-level forces
    write pot dx pymol-generated  # What to write .. this says write the potential in dx
                     # format to a file.
end
quit