[gmx-users] g_helix question
zhen at hec.utah.edu
Wed Jun 1 21:52:20 CEST 2005
On Wed, 1 Jun 2005, David wrote:
> On Wed, 2005-06-01 at 12:45 -0600, Zhen Qin wrote:
> > hi,
> > I met a problem when trying to analyse my system with g_helix function.
> > My system contains a protein (belta-helix), some membrane lipid molecules,
> > and a lot of water. I want to use g_helix to compute the helix properties,
> > so I use:
> > g_helix -f history.xtc -s system.tpr -n index.ndx
> > (my index.ndx contains atoms that form the helix).
> did you give the -ahxstart and -ahxend options?
> Always use the -h option before you run a program the first time.
Thanks alot. I tried to use -ahxstart and -ahxend before writing my last
email, but I guess I gave the wrong residue number. :-)
btw: what is purpose for the index file, since the initial and ending
residues have to be input manually?
> > However, after I ran, I found all the .xvg files excepting
> > JCaHa.xvg and helicity.xvg generated contains only
> > the informatic head, no data at all. And in helicity.xvg, the data part is
> > like
> > 1 0
> > 2 0
> > 3 0
> > 4 0
> > 5 0
> > 6 0
> > ....
> > ....
> > and all the .out files are empty.
> > This is my first time to use g_helix, I am totally confused. Are my input
> > files wrong? What shall I do?
> > Thank you very much.
> > Yours
> > Zhen
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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://xray.bmc.uu.se/~spoel
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