[gmx-users] Info on the "Ellipticity at 222 nm" provided by g_helix

David van der Spoel spoel at xray.bmc.uu.se
Wed May 3 14:25:38 CEST 2006

Afonso Duarte wrote:
> Dear All,
> I am a newbie using GROMACS and I am just going throu my first sims. I 
> have one question regarding the output of g_helix. Using this command 
> get a value for the "Ellipticity at 222 nm according to Hirst and 
> Brooks" however this value is in nm (per time frame) and for 100% 
> a-helices it shows positive values (instead of the typical negative values.
> I have read the paper from Hirst and Brooks, however I don understant 
> how can one correlate the values from GROMACS with experimental 
> ellipticity (values in mdeg and more negative when the helical content 
> increases)
> PS: I found a similar question in this newsletter, however there was no 
> reply...
Check the routine ellipticity in src/tools/hxprops.c
Right now what is plotted is the number of helical residues. There is 
also a magic number w in the data. If you have the Hirst and Brooks 
paper handy I'm sure you can fix the routine. Please send me back the 
corrected code.

> Thanks
> Afonso
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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