AMBER Archive (2009)

Subject: [AMBER] How to put another 10 ligands into the simulation system?

From: Chih-Ying Lin (chihying_at_usc.edu)
Date: Wed Dec 23 2009 - 10:51:23 CST

Hi
The system = one protein molecule + 10 ligands + water molecules in 6
x 6 x 6 box.
after 100 ns simulatin, 10 ligands have attached on the protein.

Now, I tried to put another 10 ligands into the system.
The steps are as follows.

1. Take one coordinate file and remove all the coordinates of the
water molecules.
2. Center the protein with the attached 10 ligands
3. Put another 10 ligands into the simulation box.
4. Solvate the system
5. Add ions
6. Energy minimization of the solvated system
    Turn on periodic boundary condition
   => the system is crystallized with visualization

7. Relaxation of solvent and hydrogen atom positions
   Run => Position restrained MD
   => simulation break

What is wrong here?
How to put another 10 ligands into the simulation box correctly?

Thank you
Lin

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