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)
Date: Thu Dec 24 2009 - 11:17:11 CST

On Wed, Dec 23, 2009, Chih-Ying Lin wrote:

> The system = one protein molecule + 10 ligands + water molecules in 6
> x 6 x 6 box.

What units are you using? A 6x6x6 Ang box is way too small...

> after 100 ns simulatin, 10 ligands have attached on the protein.
>
> 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.

    How did you do this?

> 4. Solvate the system
> 5. Add ions

    What commands did you use to do this?

> 6. Energy minimization of the solvated system
> Turn on periodic boundary condition

This is hard to understand: periodic boundary conditions would have been
turned on at step 4.

> => the system is crystallized with visualization

What does this mean? I don't understand the phrase "crytstallized with
viusalization"
>
> 7. Relaxation of solvent and hydrogen atom positions
> Run => Position restrained MD
> => simulation break

??? What do you mean by "simulation break"?

Basically, there is nowhere near enough information here for anyone to be of
help. You did a bunch of complicated steps, with little information (what is
the ligand? why do you want 20 of them there?) and then just say that you
had a "break" with no details of what really went wrong.

Be sure to visualize the system at step 7. A bad MD result (especially right
at the beginning of the calculation) often is the result of bad contacts
between atoms -- you can use the "checkoverlap" command in ptraj to see if
that might be the case here.

...dac

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