[gmx-users] Re: Re: g_bundle problem
Justin A. Lemkul
jalemkul at vt.edu
Sat Mar 20 00:57:43 CET 2010
Stefan Hoorman wrote:
>
>
> 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
>
>
> Right, thank you Justin, things worked out nicely now. I was able to
> calculatemy helix tilt with respect to the z axis. Would there be a way
> to calculate the tilt between two helix axes? I cannot simply calculate
> the tilt of each with respect to the z axis and subtract because the
> interhelical tilt does not depend only on the z axis. Can g_bundle give
> me that kind of information?
>
It seems like it should:
http://lists.gromacs.org/pipermail/gmx-users/2007-October/030415.html
There are other programs that calculate angles, like g_sgangle and g_angle, both
of which could potentially be used to calculate what you want.
-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
========================================
More information about the gromacs.org_gmx-users
mailing list