[gmx-users] make_ndx

Manuel Prinz manuel at pinguinkiste.de
Sun Jun 25 02:58:54 CEST 2006

Hello Dongsheng!

Am Samstag, den 24.06.2006, 17:26 -0400 schrieb Dongsheng Zhang:
> In make_ndx, I would like to keep two groups, for instance, group 4 and
> group 5. I have try it in two ways, namely, "keep 4 & keep 5" and  "keep
> 4 | keep 5". However both ways only keep group 4. Anyway to accomplish
> my task is to delete other groups one by one, but it is not so
> convenient. Could anyone tell me what is the trick? Thanks!

I don't think this can be done directly. Nevertheless, a quite simple
solution is to first copy the selections you would like to keep (by just
giving the number of the group you want to copy) and then deleting all
default groups ("del 0-13"). Your session might look like this:

> 4 [Enter]

Copied index group 4 'Backbone'

 14 Backbone            :    39 atoms

> 5 [Enter]

Copied index group 5 'MainChain'

 15 MainChain           :    53 atoms

> del 0-13 [Enter]

Removed group 0 'System'
Removed group 1 'Protein'
Removed group 2 'Protein-H'
Removed group 3 'C-alpha'
Removed group 4 'Backbone'
Removed group 5 'MainChain'
Removed group 6 'MainChain+Cb'
Removed group 7 'MainChain+H'
Removed group 8 'SideChain'
Removed group 9 'SideChain-H'
Removed group 10 'Prot-Masses'
Removed group 11 'Non-Protein'
Removed group 12 'SOL'
Removed group 13 'Other'

> [Enter]

  0 Backbone            :    39 atoms
  1 MainChain           :    53 atoms

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

> q [Enter]

The resulting index.ndx contains the desired groups.


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