[gmx-users] Re: g_bundle problem
stefhoor at gmail.com
Fri Mar 19 18:05:54 CET 2010
> Stefan Hoorman wrote:
> > I have tried using g_bundle in order to analyse helix axes in my
> > transmembran helices. I created two groups in my ndx file that included
> > the alpha carbons of the first half of my helix and a second group for
> > the alpha carbons for the second half. When I try using g_bundle the
> > following error comes up:
> > "Fatal error:
> > The size of one of your index groups is not a multiple of n"
> > What am I doing wrong?
> Not a clue - What is your exact command line? How many atoms are in each
> group? The value of n is the number of parts into which the axes are
> and there are several criteria in the code that must be met, else you get
> error. So without this information, the best guess is: some criterion is
> being met.
> > Thank you
> g_bundle analyzes bundles of axes - and therefore number of atoms each
> have to be divisible by number of axes (entered by -na). And I suppose, you
> are interested in analyzing only one axis, don't you?
Well, the exact command line was : g_bundle -f md.xtc -s md.tpr -z -n
As for analyzing one axis, yes, that is true, I am only interested in
analysing my helix principal axis.
I have tried using different group sizes for the index group. I have tried
using only carbon alpha for the first half and then for the second half
(each had 15 alpha carbons), then I tried with all sorts of different
groups, first five residues and last five residues, first fifteen residues
and so on.
All analysis came up with the same error.
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