If you can afford TI, then you should just use it.
However, make sure your TI simulation is converged, say by doubling
your simulation time for each windows, Also follow a good data
analysis procedure, which requires some reading of related literature.
Why not using the latest Amber? Its TI option should be better.
Ray
On Tue, Sep 13, 2011 at 5:33 PM, manikanthan bhavaraju
<manikanthanbhavaraju.gmail.com> wrote:
> Hi All,
>
> I have performed thermodynamic integration calculations for the
> complex(protein+ligand) system under explicit solvent conditions using ff99
> forcefield and amber8. The binding energy was -9.2 kcal/mol. There is no
> experiment value avaliable in the literature. So to cross check TI
> calculations, I have perfomed MM-GBSA and PBSA using amber11 and ff99 for
> 250 snapshots. The binding enthaplies value for GBSA was found to be -11.85
> kcal/mol. Further I have performed NAB calculations using AmberTools 1.5
> for 10 snapdhots, the entropy contribution was -19.59 kcal/mol. The net
> binding free energy for GBSA is 7.74 kcal/mol. Which is quite close to the
> TI value but with opposite sign.
>
> The PBSA binding enthaply value is nearly same as that of NAB entropy value.
>
>
> Techanically entropy value has to be far less than the present value.
> Does AmberTools1.5 typically report high entropy values? How should I
> interpet my values?
> Any suggesstions???
>
>
> Thanks,
> mani
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Received on Wed Sep 14 2011 - 10:30:08 PDT
