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 - 06:00:02 PDT
