Hello --

This is disturbing.  Could you please send the output (including the io.mc) files from your calculation with NPBE?  What version of APBS are you using?

Thanks,

Nathan

On Oct 19, 2009, at 9:00 PM, Yohei Norimatsu wrote:

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
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Nathan Baker (baker@biochem.wustl.edu)
Associate Professor, Dept. of Biochemistry and Molecular Biophysics
Director, Computational and Molecular Biophysics Graduate Program
Center for Computational Biology, Washington University in St. Louis
Web: http://bakergroup.wustl.edu/