Re: Constrain on DNA when using ABF for protein-DNA system

From: Jérôme Hénin (
Date: Fri Oct 06 2017 - 07:52:43 CDT

Dear Mahdi,

You can add a center of mass position restraint to DNA (by restraining a
distance colvar between DNA and a dummy atom located at its center). That
will not affect the correctness of the ABF calculation.

I don't know the specifics of your setup, but from what you said it might
make sense to add other restraints, particularly on the orientation of
those two molecules. It sounds like you may run into trouble if they rotate
too much.

You probably want to think about translation in X and Y as well. Actually,
in the rigid-body approximation this is a 12-degree of freedom problem, you
can get down to 6 by restraining one molecule or using internal
coordinates, and then you want to carefully consider what's going to happen
to those 6.


On 5 October 2017 at 20:25, Mehdi Bagherpour <> wrote:

> Dear NAMD users,
> I have done ABF simulation for my protein-DNA system. The DNA helical axis
> is in X direction and the distance between COM of protein and DNA is
> orthogonal to helical Axis (X), lets call Z direction.
> For doing ABF I used "distanceZ" option in colvar. When I look .dcd file
> both protein and DNA are going far from each-other in Z direction.
> My problem is: for some reasons I need DNA to be fixed in Z direction (in
> its initial position) and for that I need just protein to move far from DNA.
> Is there any solution to fix this problem without using any other
> constraint on DNA, and if it is NOT, what is the best way to constraint
> DNA without effecting on ABF results?
> Thanks,
> Mahdi

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