Hello,
There are two main things that MM/PBSA can calculate for you. You can get
binding free energies (complex, receptor, ligand -- like you pointed out)
or you can do so-called stability calculations in which there is only one
system (designated as the 'complex' in MMPBSA.py, but you don't have a
receptor or ligand).
Stability calculations reveal the relative stabilities of (at least) two
different structures/conformations.
Ultimately, a single point energy of a single structure is meaningless in
computational chemistry, since the 'zero' energy is arbitrarily chosen for
convenience. The only thing that has meaning (i.e., the only thing
measurable/observable in the lab) is a change in energy. Stability
calculations gives you the difference in (free) energy of different
conformations.
You can look at this paper for a good overview of the method:
http://dx.doi.org/10.1002/minf.201100135
HTH,
Jason
On Sat, Jul 7, 2012 at 5:54 PM, Binwu Zhao <bzhao.ncsu.edu> wrote:
> ---------- Forwarded message ----------
> From: Binwu Zhao <bzhao.ncsu.edu>
> Date: Sat, Jul 7, 2012 at 5:48 PM
> Subject: Protein aggregation energy calculation
> To: amber.ambermd.org
>
>
> Dear Amber users:
>
> I'm very new to MMPB/GBSA, I was wondering if there is a way to calculate
> the free energy of a single aggregated polypeptide chain. Because that is
> the only chain in my explicit water system. I try to learn MMPBSA's
> protocol, but what comfuses me is that there are always Receptors Ligands
> and Complex three parts. A simple system as mine, what should I do to
> calculate the only energy within the one polypeptide chain?
> I would really appreciate that if somebody could help me out.
>
> -Binwu
>
> --
> Binwu Zhao
> Dept of Chemical and Biomolecular Engineerig
> NCSU
>
>
>
>
> --
> Binwu Zhao
> Dept of Chemical and Biomolecular Engineerig
> NCSU
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> 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 Sat Jul 07 2012 - 19:00:02 PDT
