[gmx-users] Combined essential dynamics analysis

Bert de Groot bgroot at gwdg.de
Wed Jul 16 14:52:00 CEST 2003

On Wed, 16 Jul 2003, barrett wrote:

> I concluded that the problem was as follows (I could be wrong: Bert etc
> please feel free to correct):
> The change I made, removal of a phosphate makes a big difference in
> reality because it happened to be the one atom that really was holding
> the loop in place. Indeed in MD you do see the loop move when phosphate
> is removed. The program DIST however makes up lots of constraints and I
> think that in my case it made up some constraints that in fact get
> broken in nature at 300K. Therefore DIST disallowed physically
> realizable reconfigurations.
> My only suggestion is that you could go into the output of DIST and
> manually remove suspect looking constraints. However this is not very
> practical unless you know what you are looking for. Sorry.

note that Concoord and MD use very different philosophies. With MD you can
ask the question: "Given this structure, how will it develop in time?"
(and eg calculate the effect of ligand binding or similar). With
Concoord this is not possible, since it will always predict a number of
conformations AROUND a starting configuration. This implies that you
will NOT observe a structural transition if you remove e.g. a phosphate.
(at least not in the MD sense that you get a time sequence of
configurations which start in one conformation and end in another as the
simulation progresses).
And I wouldn't recommend removing constraints by  hand to force it to.

What you might do, however, is to do the simulation with and without the
ligand anyway, and look for significant differences in the ensemble
AVERAGES. Starting from the same protein configuration with and without a
ligand, this can well result in significant shifts in the average
conformation. I know a number of cases where concoord reliably predicted
protein closure around a substrate, for example.


Dr. Bert de Groot

Max Planck Institute for Biophysical Chemistry
Theoretical molecular biophysics group
Am Fassberg 11
37077 Goettingen, Germany

tel: +49-551-2011306, fax: +49-551-2011089

email: bgroot at gwdg.de

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