[gmx-users] g_bundle!

[TJ Piggot]

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 <priyankaps4 at yahoo.com> 
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 <anoddlad at yahoo.com> 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 <priyankaps4 at yahoo.com>
>> To: gmx-users at 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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----------------------
TJ Piggot
t.piggot at bristol.ac.uk
University of Bristol, UK.