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
>
>
>
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Received on Wed Jan 06 2010 - 15:00:03 PST
