On Tue, Jan 05, 2010, Chih-Ying Lin wrote:
>
> I am simulating the protein + ligand + water molecules system.
> In the experimental work, the concentration of ligand is pretty low, say
> under 20 mM (avearge 18 ligands attached on one protein)
Can you say which protein and ligand you are dealing with. In the usual
(English) meaning of these terms, a ligand would have a specific binding site
to a protein, and one would not expect multiple ligands to be bound -- are you
really dealing with extremely non-specific binding?
> It will be a huge system to create a system with 20 mM and it will take
> lot of simulation time.
The usual approach to this problem is *not* to actually simulate a 20
mM system, but rather to compute (estimate) the free energy of binding
(using just one ligand and one protein), and then to use that free energy
to compute binding probability at a given concentration. Is there some
reason this approach will not work for you?
...dac
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Received on Tue Jan 05 2010 - 05:30:02 PST
