You could also think about something like Umbrella Sampling.
On Sat, Mar 17, 2012 at 2:19 PM, Bill Miller III <brmilleriii.gmail.com>wrote:
> If the conformation of your two subunits change significantly upon binding
> than a single trajectory approach would likely not be as accurate as a
> triple trajectory approach (running MD on the complex and both subunits
> (receptor and ligand) by themselves. MMPBSA.py is able to analyze all three
> trajectories at once instead of creating those trajectories all from the
> same trajectory (single trajectory approach).
>
> I hope that helps.
>
> -Bill
>
> On Thu, Mar 15, 2012 at 8:18 PM, Wholly Peach <whollypeach.yahoo.com>
> wrote:
>
> > Dear All,
> >
> > For the on-line AMBER advanced tutorial 3 MM-PBSA, it would depend on the
> > conformation of the subunit does not change significantly. If the
> > conformation of the 2 subunits change significantly after forming the
> > complex, then we cannot get the PDB of individua subunits. Then do we
> have
> > some methods for the free binding energy calculation?
> >
> > Cheers,
> >
> > Wholly
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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Bill Miller III
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-6715
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>
--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Sat Mar 17 2012 - 12:00:04 PDT
