Re: [AMBER] NMR refinment issues

From: David A. Case <>
Date: Sat, 17 Apr 2010 04:53:44 -0400

On Wed, Apr 14, 2010, wrote:
> First time AMBER user here and am using it for NMR refinement presently.
> I followed the DNA protocol in the tutorial section and have everything
> working just fine however im having some issues with the end results.
> Im using the CALIBA macro from CYANA to cailbrate my peaklists to upper
> distance limits and when i run refinement using this anneal script

You are heating to 1000K in the simulated annealing, which is pretty high for
DNA; you should visualize your trajectories to get an idea of how deformed
the structure is at the high temperatures. That may give you some idea of
how well they can form good structures when cooled. But there is no "right
answer" here, and the nature and quality of your constraints has a big effect.

> i get small penalty values overall (~20) which from the litierature
> ive read is normal. However my the issue with my RMSD of the final
> structure, it ends up being around 1.2 which is pretty high since
> it comes out from CYANA being around .6 or so. Im not sure if my

It's not clear exactly what you mean by RMSD (pairwise average of some number
of structures? did you choose some fraction of the total number to analyze?)
But in conventional terms, an ensemble with an average RMS between pairs of
1.2 Ang. is still pretty tight. You need to decide whether or not important
information you want to learn about the structure is lost on going from 0.6
to 1.2 Ang. RMS. Details that are only present in CYANA but not in the Amber
refinement should be treated with great caution.


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Received on Sat Apr 17 2010 - 02:00:03 PDT
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