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

[Stefan Hoorman]

>
> Stefan Hoorman wrote:
>
> <snip>
>
> > 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
>
> Per the documentation, that sounds right.
>
> "The program reads two index groups and divides both of them in -na parts.
> The
> centers of mass of these parts define the tops and bottoms of the axes."
>
> -Justin
>
> > a first group for my first helix and a second group for my second helix?
> >
>

As I waited for the answer I ran some tests using: In a first analysis the
top residues for both helices in one group and the bottom residues of both
helices in another group and set the "-na" flag in g_bundle as "2".
In a second analysis I used in my first helix a the first group and the
second helix as the second group and set the "-na" flag as "4".
Both analysis were made using alpha carbons only.
I had already measured the interhelical tilt between these helices with
another program called qhelix. The problem is that it gives me loads of
problems with the sampling, since qhelix only measures each frame at a time
and I have to convert each frame into a pdb file (etc), but anyway, it gave
me interhelical tilt values that allowed me to "see" a trend there.
When I compared the results between both methods described above, the second
one gave similar results to the ones I got from qhelix.
I wrote this because maybe I understood wrong your last email, the phrase
"Per the documentation, that sounds right." refered to the sentece above or
below your statement?
Thank you
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