[gmx-users] Re: g_bundle problem
Justin A. Lemkul
jalemkul at vt.edu
Fri Mar 19 18:12:19 CET 2010
Stefan Hoorman wrote:
>
> 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 index
> group? The value of n is the number of parts into which the axes
> are divided
> and there are several criteria in the code that must be met, else
> you get this
> error. So without this information, the best guess is: some
> criterion is not
> being met.
>
> -Justin
>
> > Thank you
> >
>
> --
>
> g_bundle analyzes bundles of axes - and therefore number of atoms
> each group
> 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?
>
> Milan
>
>
> Well, the exact command line was : g_bundle -f md.xtc -s md.tpr -z -n
> bundle.ndx
> 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.
>
You're not setting the -na flag, which by default is zero. In the code, if the
value from -na (int n) is <= 0, you get the fatal error. Maybe the error
message should be made more specific, so that users actually know what n is.
You need to explicitly set a value for -na >= 1.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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