[gmx-users] make_ndx

[Dongsheng Zhang]

Hello, Manuel,

Thank you very much for your trick. It is neat.


Have a nice weekend!

Dongsheng

On Sun, 2006-06-25 at 02:58 +0200, Manuel Prinz wrote:
> 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
> 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
> 
> > q [Enter]
> 
> The resulting index.ndx contains the desired groups.
> 
> HTH
> Manuel
> 
> 
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