[gmx-users] regarding micelle and its analysis - index group

[rama david]

Hi priya

http://www.gromacs.org/Documentation/Gromacs_Utilities/make_ndx these
link may be help to you

i like to know how to calculate index groups for my micelles..

since i am having two micelles , one having 8molecules and another having
2molecules.. residue number for that 2molecule micelle is 2 and 7..

can you help me how to form index group for this two micelles..

make_ndx  command need to be used .

i searched but couldnt get the point clearly ..

make_ndx –f .....gro/pdb –o my_index.ndx
You will see the following output (we left out the descriptive info at the
beginning) followed by acommand prompt (>).

Reading structure file
Going to read 0 old index file(s)
Analysing residue names:
There are:   129    Protein residues
There are: 10824      Water residues
There are:     8        Ion residues
Analysing Protein...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting
into groups...

  0 System              : 34440 atoms
  1 Protein             :  1960 atoms
  2 Protein-H           :  1001 atoms
  3 C-alpha             :   129 atoms
  4 Backbone            :   387 atoms
  5 MainChain           :   517 atoms
  6 MainChain+Cb        :   634 atoms
  7 MainChain+H         :   646 atoms
  8 SideChain           :  1314 atoms
  9 SideChain-H         :   484 atoms
 10 Prot-Masses         :  1960 atoms
 11 non-Protein         : 32480 atoms
 12 Water               : 32472 atoms
 13 SOL                 : 32472 atoms
 14 non-Water           :  1968 atoms
 15 Ion                 :     8 atoms
 16 CL                  :     8 atoms
 17 Water_and_ions      : 32480 atoms

 nr : group       !   'name' nr name   'splitch' nr    Enter: list groups
 'a': atom        &   'del' nr         'splitres' nr   'l': list residues
 't': atom type   |   'keep' nr        'splitat' nr    'h': help
 'r': residue         'res' nr         'chain' char
 "name": group        'case': case sensitive           'q': save and quit
 'ri': residue index

>

Use the ‘r’ command to enter the list of residue numbers that represent the
N & C termini of the
triple helix.
> r 1 36 37 72 73 108
15 r_1_36_37_72_73_108 :
51 atoms
Note: You may also use a dash to specify a residue number range (e.g. to
specify residues 1 to 36
use > r 1-36) ... OR, better yet, lets specify a residue range only
including backbone atoms. Do
this with the ampersand for example ...
> r 1-36 & a C N CA
The default name (r_1_36_37_72_73_108 ) giving to the new index group that
you have just
created is cumbersome. Lets rename it using the name command. We will use
the index group #
(15) in the command.
> name 15 Terminal
> v(Verbose)
>h for help give information on index tool
>q for quite..
And use these index file by specifying it for further analysis...


you can make group by specifying atom no 0r range of atom that form micelle
..


Have a nice day........
With Best Wishes,
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