AMBER Archive (2009)
Subject: Re: [AMBER] How to put another 10 ligands into the simulation system?
From: David A. Case (case_at_biomaps.rutgers.edu)
On Wed, Dec 23, 2009, Chih-Ying Lin wrote:
> The system = one protein molecule + 10 ligands + water molecules in 6
What units are you using? A 6x6x6 Ang box is way too small...
> after 100 ns simulatin, 10 ligands have attached on the protein.
How did you do this?
> 4. Solvate the system
What commands did you use to do this?
> 6. Energy minimization of the solvated system
This is hard to understand: periodic boundary conditions would have been
> => the system is crystallized with visualization
What does this mean? I don't understand the phrase "crytstallized with
??? What do you mean by "simulation break"?
Basically, there is nowhere near enough information here for anyone to be of
Be sure to visualize the system at step 7. A bad MD result (especially right