Dear APBS Users
 
We are trying to calculate Poisson-Boltzmann profiles for ion channels. We found a perfect tutorial at: http://en.wikiversity.org/wiki/Poisson%E2%80%93Boltzmann_profile_for_an_ion_channel
The input file used for the tutorial is shown below.
 
read
         mol pqr 1OED.pqr
         mol pqr ion.pqr
         mol pqr complex.pqr
    end
    elec name protein
         mg-auto
         mol 1
         dime 97 97 97
         cglen 100.000000 100.000000 105.000000
         fglen 10 10 10   
         cgcent mol 3
         fgcent mol 2
         # NaCl ionic strength in mol/l
         ion  1 0.15 0.95 # sodium ions
         ion -1 0.15 1.81 # chloride ions

         lpbe
         bcfl mdh
         pdie 2.0 # protein and faux-lipid
         sdie 78.5 # Eisenberg and Crothers Phys. Chem. book 1979
         srfm smol
         chgm spl2
         srad 1.4
         swin 0.3
         sdens 10.0
         temp 300
         # gamma 0.105 # Uncomment for old versions of APBS -- deprecated for APBS 1.0.0
         calcenergy total
         calcforce no
    end
    elec name ion
         mg-auto
         mol 2
         dime 97 97 97
         cglen 100.000000 100.000000 105.000000
         fglen 10 10 10   
         cgcent mol 3
         fgcent mol 2
         # NaCl ionic strength in mol/l
         ion  1 0.15 0.95 # sodium ions
         ion -1 0.15 1.81 # chloride ions

         lpbe
         bcfl mdh
         pdie 2.0 # protein and faux-lipid
         sdie 78.5 # Eisenberg and Crothers Phys. Chem. book 1979
         srfm smol
         chgm spl2
         srad 1.4
         swin 0.3
         sdens 10.0
         temp 300
         # gamma 0.105 # Uncomment for old versions of APBS -- deprecated for APBS 1.0.0
         calcenergy total
         calcforce no
    end
    elec name cpx
         mg-auto
         mol 3
         dime 97 97 97
         cglen 100.000000 100.000000 105.000000
         fglen 10 10 10   
         cgcent mol 3
         fgcent mol 2
         # NaCl ionic strength in mol/l
         ion  1 0.15 0.95 # sodium ions
         ion -1 0.15 1.81 # chloride ions

         lpbe
         bcfl mdh
         pdie 2.0 # protein and faux-lipid
         sdie 78.5 # Eisenberg and Crothers Phys. Chem. book 1979
         srfm smol
         chgm spl2
         srad 1.4
         swin 0.3
         sdens 10.0
         temp 300
         # gamma 0.105 # Uncomment for old versions of APBS -- deprecated for APBS 1.0.0
         calcenergy total
         calcforce no
    end

    print energy cpx - ion - protein end
    quit
We obtained results that are identical to those displayed at the website. However, when we change lpbe to npbe (for non-linear PB), we get the energy that is ridiculously high (~ 1.0E7 kJ/mol). Is there a problem with the input file?
 
Thank you, in advance, for your assistance.
 
Regards,
 
Yohei