On 3/21/07, Mark Abraham <[EMAIL PROTECTED]> 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.
Tsjerk
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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