On Wed, Sep 10, 2008, CHAMI F. wrote:
>
> I calculated the free binding energy in implicit solvent using the MM-PBSA
> utility program. The ELE is positive which is odd cause I the structure is
> neutral. The stability calculation shows again a positive ELE .. what could
> have gone wrong?
Perhaps nothing is wrong: the total binding energy looks reasonable.
Electrostatics in molecular mechanics omits terms between atoms close in
chemical structure, so it is difficult to draw conclusions from absolute
values. The fact that the molecule is neutral is not especially
relevant here.
Since we don't have any idea what your system is, it's hard to be of
much help.
...dac
>
> # DELTA
> # -----------------------
> # MEAN STD
> # =======================
> ELE 633.75 16.99
> VDW -19.68 2.84
> INT 0.00 0.00
> GAS 614.07 14.15
> PBSUR -2.35 0.33
> PBCAL -617.61 14.85
> PBSOL -619.95 15.18
> PBELE 16.14 2.14
> PBTOT -5.89 1.03
> GBSUR -2.35 0.33
> GB -617.83 14.09
> GBSOL -620.18 14.42
> GBELE 15.91 2.90
> GBTOT -6.11 0.27
>
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Received on Fri Sep 12 2008 - 03:07:07 PDT
