[gmx-users] Re: Re: Re: g_bundle problem

[Stefan Hoorman]

>
> 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
>
> I have tried using g_sgangle, but the problem is that it does not calculate
the principal axis of the helix. Since g_sgangle allows me to choose at
maximum 3 atoms per analysis, it is quite difficult to perform such an
analysis if one is to do this for 4 or five different systems and dimers.
So, in this case, since g_bundle asks me to select a group of top and a
group of bottom atoms, I would need to create an index group with my first
group (top) being the top residues of both my helices and the second group
being the bottom residues of my helices. Or would I create a first group for
my first helix and a second group for my second helix?
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100324/4a6f0d75/attachment.html>