AMBER Archive (2008)

Subject: AMBER: Has anyone seen a protein fall apart due to PBCs?

From: David Cerutti (
Date: Tue Jan 22 2008 - 10:10:10 CST


    I'm simulating with the AMBER FF99SB forcefield, and the tetrameric
protein I've got seems to like to break into along the weaker of the two
tetramer interfaces. To be sure, there are single point mutants of this
protien known that do break along the interface in solution, but the wild
type form I've got is supposed to be stable. I've run two simulations
now; it broke apart completely in the first one, and is showing the smae
signs of instability very early in the second one.
    I am wondering if some of what I'm seeing is not a result of the
periodic boundary conditions: octahedral box, solvated initially with 14A
of water between the protein and all box edges (lots of water, so it seems
it should be pretty well insulated from periodic artifacts).
    One other thing that coul be going wrong is the fact that there are
some tails in this protein that I didn't include because they were
unresolved, and the tails each have either a glutamate or lysine reside on
    Can anyone suggest something to try to see if I can run a kosher
simulation that doesn't make the protein fall apart?


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