Re: [Apbs-users] Ridiculously high energy with npbe

[Nathan B. <ba...@bi...>]

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 (ba...@bi...)
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/