[gmx-users] g_helix question
spoel at xray.bmc.uu.se
Wed Jun 1 21:35:31 CEST 2005
On Wed, 2005-06-01 at 12:45 -0600, Zhen Qin wrote:
> 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.
> 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
> 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.
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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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