johnk at spasm.niddk.nih.gov
Tue Nov 28 16:48:25 EST 1995
In article <494j43$j25 at mserv1.dl.ac.uk>, <breeze at zeneca-ph.co.uk> writes:
|> Looking at parhcsdx.pro and comparing with parallhdg.pro reveals quite
|> a lot of differences in bond angles. These, I understand, are taken
|> largely from Cambridge Crystallographic Database small molecule crystal
|> structures in the case of parhcsdx.pro (Engh & Huber forcefield). The
|> values in parallhdg.pro, on the other hand, seem to be mainly "ideal"
|> values for tetrahedral carbons etc.
That's right. Michael Nilges and I made up the parallhdg
parameter set using ideal angles. The Engh and Huber set is far
|> My question is this: which is "right"?
Engh and Huber.
|> Do the differences matter
|> is the forcefield we use for NMR structure determination too simplistic?
|> (One might imagine that small "errors" in bond angles might propagate
|> over longer distances and contribute to experimental NOE violations,
|> for example.) Or are the effects of these small differences well within
|> the intrinsic error limits of our experimental data?
|> I just have in mind the thought that NMR structure determination is a bit
|> more heavily reliant than crystallography on "chemical knowledge" about,
|> for instance, bond angles and van der Waals radii, given its less
|> favourable observable-to-parameter ratio. If these forcefields are not
|> "right", then how "accurate" can our structures be?
Well said! NMR is more dependent on our a priori knowledge
(bond angles, vdW radii, etc.) than xtallography.
However, the improvements in bond angles and so on in the Engh
and Huber set don't really make much difference in practice. Far
more important is our poor modeling of nonbonded contacts. It
just so happens that Yours Truly is polishing off a paper on a
cute trick to improve those nonbonded contacts.
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John Kuszewski || |/ /| ||
johnk at spasm.niddk.nih.gov || / /|| ||
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that's MISTER protein G to you! |/__/| |
"Biophysics has driven me to an attitude of apocalyptic doom"
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