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).
I am still unable to understand what is meant by the "stability" analysis
using decomposition.
Thanks,
Soumya
On Tue, May 20, 2014 at 4:58 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Tue, 2014-05-20 at 10:01 +0530, Soumya Lipsa Rath wrote:
> > Thank you Jason for your reply.
> >
> > Yes, there is a bond between the complex and ligand in my case.
> However, I
> > am not trying to break any bond. Like you said, I need to find out
> > the energies of a particular segment of the complex, but, could you
> please
> > explain how to do "stability" analysis using decomposition?
>
> A "stability" calculation is a single-point energy calculation of a
> single structure (so there is only one species -- for MMPBSA.py that
> means there is only a complex, no receptor or ligand).
>
> There is an example of running a stability calculation with
> decomposition in the AmberTools test suite
> ($AMBERHOME/AmberTools/test/mmpbsa_py/08_Stability). That should help
> get you started. There is also a brief explanation in the Amber manual
> in the MMPBSA.py chapter (see the "Types of calculations you can do"
> part).
>
> Good luck,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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Received on Tue May 20 2014 - 05:00:04 PDT
