I think this is a good question that, unfortunately, I do not have a good
answer. Nevertheless, I can tell you what I am thinking.
Ideally, the structure should relax to the right one. But if you start
from a potentially wrong structure, the ions do have the potential to over
stabilize it (although theoretically it is still advisable to use them).
I am reasonably confident this should not be an issue for DNA alone if you
use monovalent ions. Although the minor-groove width can be affected by
the presence of ions, the overall structure tends to be fairly robust (as
far as short fragments are concerned).
For DNA-protein complex, this becomes a bit complicated. In this case,
divalent ions can be quite stabilizing. This is because the ions used in
our models are a bit simple and their interactions with water might be a
bit weak, they can get stuck and stabilize charged groups.
My suggestion is that unless you are sure that divalent ions are needed,
you probably like to try monovalent ions. In any case, neutralization of
the system is probably better than leaving the highly anionic system
charged. Without neutralization, the program will neutralize it for you by
spreading the counter charges across the system (e.g., all water molecules
will be slightly positively charged). This may not be desirable.
Sorry for long mumbling and hope it helps a bit.
Good luck!
yong
On Sun, 8 Feb 2004, Bill Ross wrote:
> > (i'm afraid that the ions will "over-stabilize" wrong structures
> > by creating m any local energy minima).
>
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Received on Wed Feb 11 2004 - 04:53:00 PST
