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.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
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