On Mon, Feb 13, 2012, Soumya Lipsa Rath wrote:
>
> I had one basic query regarding MMPBSA. Suppose I have to calculate the
> binding energy of a ligand to two different proteins, does the calculation
> depend on the total number of molecules of the receptor?
It's hard to understand what you are asking here. You can use mm-pbsa to
estimate the binding energy of a ligand to two different proteins. The
quality of the estimates depends on a lot of factors, but does not directly
depend on the number of atoms in the protein.
Please be aware of the limitations (as well as the promise) of the mm-pbsa
method. Here is a good recent review:
.article{Homeyer12,
author = {Homeyer, Nadine and Gohlke, Holger},
title = {Free energy calculations by the Molecular Mechanics Poisson−Boltzmann
Surface Area method},
journal = {Mol. Informatics},
volume = {DOI: 10.1002/minf.201100135},
year = {2012}
...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Feb 13 2012 - 05:30:01 PST
