[gmx-users] How to create three different zones to minimize energy of a enzyme?

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Mar 19 08:34:29 CET 2008

Hi Lacerda,

You should be cautious in the interpretation of your results. Your
active site will only be minimized in potential energy in the context
of your frozen surface and your restraint internal degrees of freedom.
You should be very confident that your surface is about correct and
your internal dof are approximately correct in relation to the state
of the active site you're interested in. And that's only in terms of
energy minimization. If it comes to dynamics, using this approach you
would disallow the larger amplitude motions of your system and
therefore the coupling with the active site, or actually the
meaningful dynamics of the active site.

Now, say you want to energy minimize the active site because you put a
ligand in. In most cases, the ligand will alter the ensemble. It may
very well commute with residues on the surface (allostery?). If you
constrain residues which are to respond to the ligand you will add
strain to the system which wouldn't be there in the real
(unconstrained) thing. You can imagine how this works by placing two
magnets together with the equal poles, while constraining them, rather
than leaving one to respond to the other.

Hope this helps,


On Wed, Mar 19, 2008 at 1:51 AM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> Evanildo Júnior wrote:
>  > Dear gmx-users,
>  >
>  > I would like to minimize the potential energy of the active site of an
>  > enzyme. Because I do not have too much computer power to perform a full
>  > enzyme calculation, I need to create three different zones in which the
>  > calculation will take place. The first one is  the outer boundary of the
>  > enzyme that will remain frozen during the calculation.
>  Look for "freeze groups" in the manual. They work with MD and I'm
>  guessing they also work with EM.
>  > The second one is
>  > a transition region between the active site region and the outer
>  > boundary, whose atoms will receive a parabolic potential in order to
>  > move just a little bit.
>  Use position restraints.
>  > The last one is the active site itself which
>  > will be freely minimized. I would like to know how do I implement it in
>  > practice. Does anyone has a Gromacs script for this task? The other
>  > question is how do I freeze only the C-alpha chain?
>  Apply a freeze group only to the C-alpha atoms. You'll need to use
>  make_ndx to make the group and give that index file to grompp as well as
>  the usual stuff.
>  If you're as new to GROMACS as you sound like you might be, you should
>  do some tutorial material and read the first few chapters of the manual
>  thoroughly. Doing the above would not be a good way to get your first
>  exposure to using GROMACS.
>  Mark
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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