Re: ¶^¬–°GRe: [AMBER] low concentration simulation ?

From: <steinbrt.rci.rutgers.edu>
Date: Thu, 7 Jan 2010 05:32:09 -0500 (EST)

Hi,

> "If you need 18 ligands attached just start that way and forget about the
> "concentration" of the ligand."
>
> so, you agree with me ?
> I remove the water moleucles from the system, add other ligands, put water
> molecules into system again?

I guess what Dean wanted to say is, if you put 18 ligands (2.99E-23 mol)
into a 6nm^3 box (2.16E-22 l), then your ligand concentration will be 138
mM, not 20 mM, so I guess no, what you say is not a good way to set up a
low concentration simulation.

As other people have suggested before, it may be a good idea to go back to
the experimental data you have and check where the number of 18 ligands
comes from. It would be highly unusual for a protein to stochiometrically
bind 18 ligands, so if this really is the process you want to simulate, it
would be something of a novel project...

Kind Regards,

Thomas

Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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Received on Thu Jan 07 2010 - 03:00:02 PST
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