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

From: Vlad Cojocaru (
Date: Fri Oct 06 2017 - 08:08:33 CDT

Dear Mahdi,

Did you try instead of the distanceZ, a sort of minimal distance
(defined using distanceInv) ? In our systems, using such an order
parameter does not need any additional restraints ... Also, as Jerome
pointed out, distanceZ may not correctly describe your motion as the
unbinding is very unlikely to be straight. On the other hand, this
problem you may have with a minimal distance as well depending on how
you define it ....

A straight unbinding is likely to give you reasonable free energy
barriers only if used in combination with Chris Chipot and Benoit Roux's
scheme with lots of restraints for which you have to later extract their
contribution to PMFs (see their JCTC papers from 2-3 years ago).
However, I am not aware of any study of this approach on a protein-DNA
system, which are more complicated than the systems published...

On the other hand, if you are interested also in the unbinding pathway
and not only in the numbers, the straight unbinding may not be the way
to go forward ....


On 10/06/2017 02:52 PM, Jérôme Hénin wrote:
> 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.
> Jerome
> 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

Vlad Cojocaru, Ph.D., Project Group Leader
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]

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