[gmx-users] chemical shift and dipolar

David van der Spoel spoel at xray.bmc.uu.se
Fri Mar 8 14:17:43 CET 2002

On Thu, 7 Mar 2002, YUJIE WU wrote:

>Hi there,
>I am wondering how to calculate two quantities from a MD simulation:
>15N anisotropic chemical shift and 15N-1H dipolar for an alpha helix.

First of all, this is non trivial and the quantum chemistry to do this is 
complicated. That said, there are some empirical methods implemented in 
GROMACS. In the do_total program 1H chemical shifts can be computed, it 
uses the program TOTAL from Mike Williamson, see M P Williamson and T 
Asakura, J Magn Reson Ser B 101 63-71 1993

ANother even simpler alogirhtm is based on purely phi/psi angles and that 
works really only for folded proteins, that is implemented in g_chi.
(this gives four different backbone shifts).

I would encourage you to check recent work of David Case (www.scripps.edu)

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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