[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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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