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

[Justin A. Lemkul]

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?
> 


-- 
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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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