HI
>From Dean Cuebas;
"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?
Thank you
Lin
----- 原有信件 -----
寄件者: Dean Cuebas <deancuebas.missouristate.edu>
日期: 星期四, 2010 年 1 月 7日, 上午 6:49
主旨: Re: [AMBER] low concentration simulation ?
收件者: AMBER Mailing List <amber.ambermd.org>
> Dear Chih-Ying,
>
> I understand that in order to have 20mM of your ligand, you
> require only 2.6
> ligands in your 6x6x6nm in your water box, so that in order to
> have 18
> ligands you'd need a water box 7 times larger, which is
> prohibitive in
> computational cost.
>
> Do not think of it that way.
>
> If you need 18 ligands attached just start that way and forget
> about the
> "concentration" of the ligand.
>
> My 2cents, and good luck with your work!!!
>
> Dean
>
> Dr. Dean Cuebas, Associate Professor of Chemistry
> deancuebas.missouristate.edu, Ph 417-836-8567 FAX 417-836-5507
> Dept. of Chemistry, Missouri State University
> Springfield, Missouri 65897
>
>
>
> > From: Chih-Ying Lin <chihying.usc.edu>
> > Reply-To: AMBER Mailing List <amber.ambermd.org>
> > Date: Wed, 6 Jan 2010 15:30:32 -0600
> > To: AMBER Mailing List <amber.ambermd.org>
> > Subject: [AMBER] low concentration simulation ?
> >
> >
> >
> > HI
> > 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)
> > It will be a huge system to create a system with 20 mM and it
> will take lot of
> > simulation time.
> >
> > Instead, I create a 6nm x 6nm x 6nm simulation box and put one
> protein> molecule with 10 ligands.
> > After 100 nano seconds, 10 ligands are attached on the protein.
> >
> >
> > Then, for this one protein with 10 ligands attached + water
> molecules> I will do the following steps =>
> > 1. remove the water molecules
> > 2. center the protein with 10 ligands attached in the 6nm x 6nm
> x 6nm
> > simulation box
> > 3. put another 10 ligands around the protein with 10 ligand attached
> > 4. solvate the system
> > 5. add ions
> >
> >
> > Are the above steps make sense to create a low concentration
> simulation?>
> > Thank you
> > Lin
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
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Received on Wed Jan 06 2010 - 16:00:02 PST
