[gmx-users] g_bundle!

[Patrick Fuchs]

Hi,
I wrote a program to calculate the tilt angle between a helix axis and 
the bilayer normal called g_tilt. It's available here 
http://condor.ebgm.jussieu.fr/~fuchs/download/. There you'll find also a 
program to calculate the azimuthal rotation (g_rotation).
I plan to upload these contributions on the GROMACS website when I have 
time :-)
Ciao,

Patrick

priyanka srivastava a écrit :
> Dear All,
>
> I want to calculate tilt angle of a peptide inserted
> inside the lipid bilayer (i.e. angle between the
> helical axis and bilayer normal). From previous posts
> I got an idea that g_bundle wud solve my problem.
>
> I am issuing the following on the command line:
>
> g_bundle -f test.xtc -s test.tpr -na 2 -z -tu ps
>
> This asks me to "Select a group of top and a group of
> bottom atoms"
>
> Group     0 (      System) has 12877 elements
> Group     1 (     Protein) has   102 elements
> Group     2 (   Protein-H) has    79 elements
> Group     3 (     C-alpha) has    10 elements
> Group     4 (    Backbone) has    31 elements
> Group     5 (   MainChain) has    41 elements
> Group     6 (MainChain+Cb) has    49 elements
> Group     7 ( MainChain+H) has    54 elements
> Group     8 (   SideChain) has    48 elements
> Group     9 ( SideChain-H) has    38 elements
> Group    10 ( Prot-Masses) has   102 elements
>
> when I chose "1" and "1" it gives all angles as 90,
> which is wrong and bun_tiltr is reported as "nan". The
> manual says that "the program reads two index groups
> and divides both of them in -na parts".
> I am a lil confused! what should be my choice here?
>
> regards,
> Pri...
>
>
>
>
>        
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-- 
_______________________________________________________
Patrick FUCHS
Equipe de Bioinformatique Genomique et Moleculaire
INSERM U726, Universite Paris 7
Case Courrier 7113
2, place Jussieu, 75251 Paris Cedex 05, FRANCE
Tel : +33 (0)1-44-27-77-16 - Fax : +33 (0)1-43-26-38-30
E-mail : Patrick.Fuchs at ebgm.jussieu.fr
Web Site: http://www.ebgm.jussieu.fr/~fuchs