[gmx-users] Restrict Terminal of protein?

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Mar 21 12:57:53 CET 2007

On 3/21/07, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> Tsjerk Wassenaar wrote:
> > Hi Qiang Zhong,
> >
> > You can use position_restraints or define distance_restraints (Chapter
> > 5). But will you get meaningful results?
> ... by which Tsjerk refers (among other things) to the observation that
> the rest of the protein is much more than just a scaffold for this
> receptor to hang from. The electrostatic environment it creates is quite
> different from the solvent. You're unlikely to generate meaningful
> results without the scaffold there, or demonstrate that you've done so.
> Holding the scaffold fixed is another matter though...

That will "only" change your conformational probability density
function to a CONDITIONAL pdf, with a likely restriction of the
sampling of regions you may well be interested in. Always caution when
playing tricks like that.


> 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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