AMBER Archive (2007)

Subject: Re: AMBER: Tutorial for chemical shift calculation?

From: Mike Summers (summers_at_hhmi.umbc.edu)
Date: Tue Feb 06 2007 - 12:36:05 CST

David,

Wow, I'm really behind the times. Your web site did the trick.

Many thanks,

Mike

On Tue, Feb 06, 2007 at 08:25:40AM -0800, David A. Case wrote:
> On Mon, Feb 05, 2007, Mike Summers wrote:
>
> > I'd like to calculated the chemical shift of a
> > methyl group within a protein. Based on my reading
> > of the Amber9 manual, I think I should use DivCon, but
> > I can't find examples on how to execute DivCon,
> > how to set up the input files, etc. Some examples I've
> > found suggest that DivCon is executed from within Antechamber.
> >
>
> There are two ways in Amber that one can compute the chemicals shifts of the
> protons in a methyl group. [Neither one is well documented :-( ]
>
> 1. You can use empirical formulas that compute ring current, electrostatic,
> and peptide group contributions. This is basically the model in this paper:
>
> %A K. Ösapay
> %A D.A. Case
> %T A new analysis of proton chemical shifts in proteins
> %J J. Am. Chem. Soc.
> %V 113
> %P 9436-9444
> %D 1991
>
> In spite of its age, this actually does quite a good job for methyl protons in
> proteins, (see Table III of the above paper) and (as far as I know) has not
> been superceded by more recent work. I am pretty close to having a tutorial
> prepared on how to do this in Amber. [The code in Amber is not broken, but
> it's a bit tricky to prepare the needed input -- that's why my promise to get
> this done is not quite there yet.]
>
> If you just want a result for a few conformations, you can use the web
> service at http://www.scripps.edu/mb/case/qshifts/qshifts.htm, or download
> the SHIFTS code (same web site) and run it locally.
>
> 2. You can also use the semiempirical quantum chemical code (DivCon) in Amber
> to do this calculation. This would give estimates for both carbon and proton
> shifts. The basic literature papers are here:
>
> %A B. Wang
> %A E.N. Brothers
> %A A. van der Vaart
> %A K.M. Merz
> %T Fast semiempirical calculations for nuclear magnetic resonance chemical
> %shifts: A divide-and-conquer approach
> %J J. Chem. Phys.
> %V 120
> %P 11392-11400
> %D 2004
>
> %A B. Wang
> %A K.M. Merz, Jr.
> %T A fast QM/MM (quantum mechanical/molecular mechanical) approach to
> calculate nuclear magnetic resonance chemical shifts for macromolecules
> %J J. Chem. Theory Comput.
> %V 2
> %P 209-215
> %D 2006
>
> I haven't used this myself, but there is a sample calculation in
> the amber9/test/crambin_qmmmnmr subdirectory. This may be enough to get you
> started. Since this is a semi-empirical model, you'll want to read the above
> papers carefully to get some idea of the expected accuracy.
>
> ...hope this helps....dac
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-- 

*********************************
Michael F. Summers
Department of Chemistry and Biochemistry
  and Howard Hughes Medical Institute
University of Maryland Baltimore County
1000 Hilltop Circle 
Baltimore, MD 21250

Phone: (410)-455-2527  
FAX:   (410)-455-1174
Email: summers_at_hhmi.umbc.edu
Web:   www.hhmi.umbc.edu
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