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 - 04:30:02 PDT
