MMPBSA.py allows you to specify only a complex (so no receptor or ligand),
and it will just give you the statistics for that one trajectory. If you
cluster your simulations and collect "folded" and "unfolded" snapshots, then
you can run MMPBSA.py on each of these clusters and get, roughly speaking,
your free energy of folding. (Be aware of MMPBSA shortcomings, though).
HTH,
Jason
On Fri, Sep 2, 2011 at 1:43 PM, KIRTANA S <skirtana4.gmail.com> wrote:
> Hi Thomas,
>
> MMPBSA calculates the change in binding free energy of the ligand and
> receptor.
> How can I use this only for the complex only.
>
> Thanks
> kirtana
> Fri, Sep 2, 2011 at 2:43 AM, <steinbrt.rci.rutgers.edu> wrote:
> > Hi Kirtana,
> >
> > you can use MM-PBSA for that purpose. There is a tutorial on how to use
> it
> > on the Amber page plus some examples in the $AMBERHOME/src/mmpbsa
> > directory. But note that it will be very difficult to get the correct
> > ensemble for your unfolded state.
> >
> > Kind Regards,
> >
> > Thomas
> >
> > On Thu, September 1, 2011 4:09 pm, KIRTANA S wrote:
> >> I want to calculate the free energy change while my polymer folds.
> >> I have used Implicit solvent, explicit solvent and also vacuum for my
> >> simulation .
> >>
> >> How can I get the energy of the complex only throughout the simulation
> >> run.
> >>
> >> Thanks in advance
> >> kirtana
> >>
> >> _______________________________________________
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> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> > Dr. Thomas Steinbrecher
> > formerly at the
> > BioMaps Institute
> > Rutgers University
> > 610 Taylor Rd.
> > Piscataway, NJ 08854
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Sep 02 2011 - 11:00:05 PDT
