dong at pampas.chem.purdue.edu
Sun Jun 25 03:38:20 CEST 2006
Thank you very much for your trick. It is neat.
Have a nice weekend!
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
> '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.
> gmx-users mailing list gmx-users at gromacs.org
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
More information about the gromacs.org_gmx-users