AMBER Archive (2006)

Subject: Re: AMBER: MMPBSA: magnitude of PB calculation

From: sishi.tang_at_utoronto.ca
Date: Sat Feb 04 2006 - 10:47:21 CST

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_at_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_at_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.
> >
> >
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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_at_uci.edu
> Home page: http://rayl0.bio.uci.edu/rayl/
> ====================================================
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