AMBER Archive (2005)

Subject: Re: AMBER: GB refinement of CYANA structures

From: David A. Case (case_at_scripps.edu)
Date: Fri Sep 16 2005 - 16:40:37 CDT

On Fri, Sep 16, 2005, Eugene DeRose wrote:
>
> I would like to refine CYANA structures using generalized Born solvent
> refinement. Bin Xia, et al., JBNMR 22, 317-331, 2002, describe such a
> procedure, but the experimental discussion does not give a detailed
> account of the GB MD refinement protocol. Can anyone refer me to a
> more detailed account of a GB MD protocol for refining NMR structures?

There is no one preferred protocol; generally, procedures that work for
"gas-phase" refinements should provide a good start for GB refinements as
well. Some experimentation is usually required for each system(particularly
for how high a temperature to use, and how slowly to cool).

...good luck...dac

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