[Apbs-users] Sign of Electrostatics energy using APBS

[Pralay M. <pr...@ri...>]

Hi,

I am computing electrostatic energy using APBS (Version 1.0.0). But, the
total electrostatic energy it shows as a positive value. I am even more
surprised to see that the difference in electrostatic energy of a complex
(PDB:1ATN) and its subunit is positive (Global net ELEC energy =
3.715578077044E+05 kJ/mol).

I think I am not interpreting it properly! Anybody can explain this please?
Thanks in advance.


I am using Fedora Core 5 and the input file to APBS is:

read
         mol pqr 1ATN_r_b.ent.pqr
         mol pqr 1ATN_l_b.ent.pqr
         mol pqr 1ATN.ent.pqr
    end
    elec name subunit1
         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 subunit2
         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 complex
         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 complex - subunit1 - subunit2 end
    quit


regards,
PRALAY MITRA



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