Ellipticity 222 - negative values?

User discussions
1

Hi all,

I have a question about the positive value of the output of the ellipticity 222 Θ_222 , as an output from the gmx helix package.

Specifically, I run

“gmx helix -s top.tpr -n index.ndx -f traj.xtc -b 400000 -cz conf.gro”

and got the “cd222.xvg” file like this:

"# gmx helix is part of G R O M A C S:

Great Red Oystrich Makes All Chemists Sane

@ title “Ellipticity at 222 nm”
@ xaxis label “Time (ps)”
@ yaxis label “nm”
@TYPE xy
400000 59.57
400050 60.32
400100 57.64
400150 59.94
400200 60.63
400250 56.91
400300 56.67…".

Why is the output value of the ellipticity positive, instead of being negative? Since according to Hirst and Brooks (1994) (DOI: 10.1006/jmbi.1994.1644), the ellipticity is negative (Table 2/ page 176).
May someone have any explanation, please?

Many thanks,

Anh Mai

2

Hi Mai,

In the paper that you cite, GROMACS takes equation (4), but only calculates the \sum w term and uses k=0.

You will have to multiply these terms with V_infty / N_r, where N_r is the number of residues in the protein.

V_infty is given in the paper as -42,000 deg cm^2 dmol^-1

Then you should see the negative values in the order of magnitude that you’d expect from the data in the paper.

1 Like
3

Thanks a lot, @cblau. ^^