use the program make_ndx or just edit the .ndx file using a text editor
Tom
--On 21 June 2007 11:03 -0700 priyanka srivastava <[EMAIL PROTECTED]>
wrote:
Does this mean defining my own .ndx file and not using
the default one?
If yes, can you please drop some hints of how to make
the .ndx file for this purpose.
thanks and regards,
Pri...
--- Alan Dodd <[EMAIL PROTECTED]> wrote:
I've used g_bundle a lot for just this sort of
thing. You need to define the top and bottom of the
helix as seperate groups, and define them *very*
carefully - it does make a difference how you do it,
presumably because g_bundle just plots the axis
between the COM of both groups? I usually define as
close to 1 complete turn of the backbone of the
helix at each end as possible.
Your output is not surprising, given what you've
asked the program for - the axis between two points
that precisely overlap ;-)
----- Original Message ----
From: priyanka srivastava <[EMAIL PROTECTED]>
To: gmx-users@gromacs.org
Sent: Wednesday, June 20, 2007 3:27:42 PM
Subject: [gmx-users] g_bundle!
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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University of Bristol, UK.
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