Chih-Ying Lin wrote:
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. With "genbox" command, to put another 10 ligands into the simulation box.
4. Solvate the system, with "genbox" command
5. Add ions, with "genion" command
6. Energy minimization of the solvated system
pbc = xyz (minim.mdp)
=> the system is crystallized with visualization
What's the energy and maximum force?
7. Relaxation of solvent and hydrogen atom positions
Run => Position restrained MD
=> simulation break
Check the box size at each step makes sense. Load the structure at each
step into a visualization program and check that it makes sense with the
box. I'm expecting you've got some molecule clashing with another. If
everything's OK, trying a smaller integration time step can sometimes help.
Otherwise, the procedure looks good.
Mark
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