Thank you so much for the simplification.
Thanks,
Soumya
On Tue, May 20, 2014 at 6:15 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Tue, 2014-05-20 at 17:19 +0530, Soumya Lipsa Rath wrote:
> > Thanks for the reply, but I don't want to calculate the stability of the
> > complex. And if I use per-residue decomposition for this analysis, the
> > interaction energy of each residue to the total complex would be
> calculated
> > (which also includes aminoacids from the ligand part).
>
> In MM/PBSA terminology, a "complex" refers to the NON-covalent
> interaction between two different molecules -- a 'receptor' and a
> 'ligand'. If there is a bond between what you call a "receptor" and
> what you call a "ligand", then you cannot use the standard
> complex-receptor-ligand MM/PBSA approach to obtain even qualitatively
> reliable results. At all.
>
> > I am still unable to understand what is meant by the "stability" analysis
> > using decomposition.
>
> "Stability" calculations in MM/PBSA analyses are _just_ single-point
> energy calculations of a SINGLE species (i.e., no "free receptor and
> ligand"). That is all. Such calculations are most commonly used to
> compare the relative stability of multiple conformers by comparing the
> energies, which is where the term "stability calculation" comes from.
> If you only provide a complex topology file (and no receptor or ligand),
> MMPBSA.py will give you JUST energies for that one system.
>
> If you choose per-residue decomposition, you will get the contribution
> of each residue toward the total energy (of the whole system). If you
> choose pairwise decomposition, you get pairwise interactions between
> specific pairs of residues in your system.
>
> >From the sound of it, your problem simply cannot be cast in terms that a
> the standard MM/PBSA approach can treat. If you can take advantage of
> some of MMPBSA.py's functionality to compute some specific energies that
> you need for part of your analysis, then you can use MMPBSA.py for that.
> I only mentioned stability-decomposition calculations because that is
> the only calculation I can think of that might give you values you can
> qualitatively interpret. If you either cannot understand what these
> calculations are or what they mean, or if these values are not what you
> are trying to compute, then the MM/PBSA scripts (mm_pbsa.pl and
> MMPBSA.py) are not appropriate tools for your problem.
>
> Good luck,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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Received on Tue May 20 2014 - 07:00:03 PDT
