You should set the dielectric constant of the complex, the receptor, and
the ligand to 2 at a minimum, and perhaps to 4 (see Ray Luo's response).
You're modeling the ligand as a vacuum right now, which could explain the
high PB contribution, due to lack of screening. The solvent portion should
be set to 80.
Natasja Brooijmans, Ph.D.
e-mail: nbrooij.itsa.ucsf.edu
On Sat, 4 Feb 2006 sishi.tang.utoronto.ca wrote:
> Hi Dr. Luo,
>
> I'm using Amber 7. The dielectric constant of the ligand was set to one. For a
> nonpolar compound with multiple aromatic rings, I don't imagine there will be
> a lot of charge-charge interactions. So is there any significant change for
> the MM-PBSA script of AMBER 7 vs. Amber 8 with the bugfixes? If not, I'll try
> to use a dielectric constant of 4 and see what happens.
>
> Thanks a lot for your help!
> Sishi.
>
>
>
>
> Quoting Ray Luo <rluo.uci.edu>:
>
> > Sishi,
> >
> > First thing first, have you patched all bugfixes for Amber8?
> >
> > If yes, what dielectric constant did you use? Do you have lots of
> > charged interactions at the binding interface? If the binding interface
> > is dominated by charge-charge interactions, previous experiences show
> > that a higher dielectric constant at least 4 should be used to
> > compensate the lack of rotation polarization (which screens down
> > charge-charge interactions) due to the insufficient sampling of backbone.
> >
> > Ray
> >
> > sishi.tang.utoronto.ca wrote:
> >
> > >Hi all,
> > >
> > >I'm calculating the binding energy of a protein with a nonpolar ligand
> > using
> > >MMPBSA, the results that I obtained are as follows:
> > >
> > >ELE -27.41 3.62
> > >VDW -52.37 2.66
> > >INT 0.00 0.00
> > >GAS -79.78 4.73
> > >PBSUR -3.37 0.22
> > >PBCAL -573.75 28.49
> > >PBSOL -577.12 28.40
> > >PBELE -601.16 27.46
> > >PBTOT -656.90 26.82
> > >
> > >I also performed entropy calculation using nmode, which results in an
> > entropy
> > >contribution of around -5 kcal/mol (T=298) If that's the case, the overall
> > >absolute binding energy amounts to -650 kcal/mol,which is obviously
> > >non-physical. Is there any obvious anormaly in my PB results? Any
> > >suggestions/advice will be more than welcome.
> > >
> > >Thanks,
> > >Sishi.
> > >
> > >
> > >-----------------------------------------------------------------------
> > >The AMBER Mail Reflector
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> > >
> > >.
> > >
> > >
> > >
> >
> > --
> > ====================================================
> > Ray Luo, Ph.D.
> > Department of Molecular Biology and Biochemistry
> > University of California, Irvine, CA 92697-3900
> > Office: (949)824-9528 Lab: (949)824-9562
> > Fax: (949)824-8551 e-mail: rluo.uci.edu
> > Home page: http://rayl0.bio.uci.edu/rayl/
> > ====================================================
> >
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>
>
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Received on Tue Feb 07 2006 - 06:10:05 PST
