AMBER Archive (2008)

Subject: RE: AMBER: binding energy: high ELE

From: CHAMI F. (fatima.chami_at_durham.ac.uk)
Date: Thu Sep 11 2008 - 12:24:23 CDT

-----Original Message-----
From: owner-amber_at_scripps.edu on behalf of David A. Case
Sent: Thu 11/09/2008 16:42
To: amber_at_scripps.edu
Subject: Re: AMBER: binding energy: high ELE
 
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?

Thanks for replying.

Perhaps nothing is wrong: the total binding energy looks reasonable.

yes, it is close to the value calculated in explicit solvent.

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.

The system is composed of a stack of planar molecules ( like in DNA strand ), each molecule is of a net charge -2.
The trajectories were extracted from an MD simulation with Na+ counter-ions.

I have a question about how to solve an ionic solute in implicit solvent ....( which parameters are to set to non default in the
PB or GB solvent.

best wishes
Fatima

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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