From: Rebecca Perlow <rp284_at_SCIRES.ACF.NYU.EDU>
Date: Mon 22 Mar 1999 19:42:06 -0500

Dear Amber users,
I posted a question a couple of weeks ago regarding counterions to be used
during an MD simulation of a protein/DNA complex. Many members of the
list e-mailed me expressing interest in this topic and asking for any
useful advice that i came across.

Basically, the advice I received pointed towards neutralizing the complex
as a whole, not the DNA individually before insertion into the protein.
The way to go about this depends very much how much work you want to
invest. Here is a summary of the advice that I received from Eberhard von
Molecular dynamic simulations with ions only makes sense if
you include explicit water. If you would like to neglect water, you
have to use Langevin dynamics.

A "simple" method to include explicit water and counterions:

1) Make a short dynamic simulation of the complex with water but
without ions.

2) Omit all water molecules in direct contact to the protein or
DNA atoms, or ions. Calculate the electric energy of the oxygens
of the water molecules. The oxygen with the absolute highest energy
is replaced by an ion, by a cation if the energy is positive, or
by an anion if it is negative.

3) Short version: Go back to 2 until you have placed all your

4) Fill the remaining free spaces with water molecules, and make a
short energy minimization run to get rid of initial strain etc...

5) Long version: Go back to 2 until you have placed all your

6) Carefully equilibrate your system.

In a more elaborate version you could make a browian dynamics
simulation with the protein and DNA fixed, no water, and the
ions moving around the complex until equilibration. In this
case you could use different ion distributions as different
starting points for your complete simulation.

Hope this helps. Also let me know if anyone else has other suggestions.

-Rebecca Perlow
Received on Mon Mar 22 1999 - 16:42:06 PST
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