Patrick.Fuchs at ebgm.jussieu.fr
Wed Jun 20 16:59:11 CEST 2007
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
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?
> Yahoo! oneSearch: Finally, mobile search
> that gives answers, not web links.
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