THANKS -- Re: AMBER: NMR vs. X-ray structures

From: Sally Pias <>
Date: Wed, 13 Jun 2007 22:33:06 -0600

Thanks to Marc Baaden and Carlos Simmerling for your help with this
issue. Your suggestions have given me a helpful starting place.


Sally Pias

On 6/11/07, Sally Pias <> wrote:
> I am wondering whether anyone knows of a systematic study of the
> behavior of NMR versus X-ray protein structures during MD simulations.
> I noticed in the amber reflector archives that NMR structures are
> known to have a tendency to show less stability than X-ray structures
> (per Yong Duan, October 2003). I am looking for any publications that
> may demonstrate this trend and that may offer some explanation for it.
> Otherwise, I would be grateful for any explanation that you all might
> offer.
> I have naively carried out a series of MD simulations starting with an
> NMR protein structure (wild-type and in silico point mutants), using a
> 20 ps equilibration to 300 K. During subsequent 5 ns production runs,
> I am seeing RMSD's averaging 4 to 6 Angstroms. I later carried out
> identical simulations on a homologous protein, for which both NMR and
> X-ray structures exist. While the NMR structure again gave an RMSD
> peaking at 6 Angstroms over 5 ns, the X-ray structure's RMSD reached
> only 1.5 Angstroms over the same timescale.
> Do you think that a longer, more elaborate equilibration would lessen
> this discrepancy? Can I trust any of the NMR-based data I have
> gathered so far, or is the RMSD out of a believable range?
> Thank you for your help.
> Sally
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Received on Sun Jun 17 2007 - 06:07:16 PDT
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