Was the nmr done in the presence of the protein? If not, then the
simulation won't match the experimental conditions anyway so any of the
models is probably as good as another. If you are simulating the same
conditions as experiment, then I would choose the model that best
reproduces the nmr data. If you did the nmr, you know this best.if not,
then read the article describing the refinement (or ask the person who did
it if there is no article). If these don't work, you might want to measure
yourself how well each model reproduces the experimental data. In the end
you will likely find that for a docking study the differences between the
nmr-based models will not be the limiting factor in the quality of the
results.
On Feb 2, 2016 7:30 AM, "ankita mehta" <mehtaroadies.gmail.com> wrote:
> Yah, My question is on how to decide which model to keep ?
> I want to go for minimization next and then for the protein docking ....to
> study the role of the protein..
> Thanks in advance!
>
>
> On Tue, Feb 2, 2016 at 5:50 PM, Jason Swails <jason.swails.gmail.com>
> wrote:
>
> > On Tue, Feb 2, 2016 at 6:18 AM, ankita mehta <mehtaroadies.gmail.com>
> > wrote:
> >
> > > Dear ALL,
> > > I have a NMR solved PDB structure which has 20 models.
> > > I want to proceed for minimization.
> > > Please let me know how to pick one representative out of all these?
> > >
> >
> > It's unclear what you're asking. Are you asking how do you create a
> file
> > that has only a single model? Well the way I would do it is to copy the
> > PDB file and then delete all of the models I didn't want inside a text
> > editor. There are other ways (e.g., using cpptraj), but the way I
> > described is conceptually quite simple and you can be sure that you are
> > doing what you want.
> >
> > If you're asking how do you decide which model to keep, then my answer is
> > "keep the best one". Of course that's a subjective criteria -- only you
> > can decide which model is best for your application (or if the
> differences
> > between the models really even matter).
> >
> > HTH,
> > Jason
> >
> > --
> > Jason M. Swails
> > BioMaPS,
> > Rutgers University
> > Postdoctoral Researcher
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Tue Feb 02 2016 - 05:00:03 PST
