[gmx-users] Help with editconf

[Catarina A. Carvalheda dos Santos]

Rita,

If that's so then I'm afraid that either your make_ndx has some problem or
you're typing something wrong.
You can try doing the same with different input files and/or different
GROMACS versions, but the second option is the most likely one.

Sorry that I cannot help you further.

Cheers,

On 17 December 2015 at 14:30, Rita Galvão <ritamelo at ctn.ist.utl.pt> wrote:

> Thanks Catarina,
>
> I have tires but the programme only consider the first number. Take your
> example, make_ndx only consider group with 0 (protein).
>
> I am using gromacs 5.0.4
>
> Obrigada :)
>
> Rita
>
> No dia 17/12/2015, às 11:27, "Catarina A. Carvalheda dos Santos" <
> c.a.c.dossantos at dundee.ac.uk> escreveu:
>
> > Consider the following groups in an imaginary .ndx file:
> >
> > 0 Protein
> > 1 Lipid_1
> > 2 Lipid_2
> > 3 Lipid_3
> > 4 SOL
> >
> > To create a new group with the protein and the 3 types of lipids using
> > make_ndx:
> >
> > 0 | 1 | 2 | 3
> >
> > This will create a new group containing groups 0, 1, 2 and 3.
> >
> > On 17 December 2015 at 11:13, Rita Galvão <ritamelo at ctn.ist.utl.pt>
> wrote:
> >
> >> Thanks Tsierk!
> >> My problem is in gmx make_ndx. I need to create to group, one with the
> >> protein and other with  protein and 3 kind of lipids excluding waters.
> >> Do you know how to do?
> >> Rita
> >>
> >> No dia 16/12/2015, às 20:47, Tsjerk Wassenaar <tsjerkw at gmail.com>
> >> escreveu:
> >>
> >>> Hi Rita,
> >>>
> >>> You'll need to make/use an index file (gmx make_ndx).
> >>>
> >>> Cheers,
> >>>
> >>> Tsjerk
> >>>
> >>> On Wed, Dec 16, 2015 at 7:06 PM, Rita Melo <ritamelo at ctn.ist.utl.pt>
> >> wrote:
> >>>
> >>>> Dear all,
> >>>>
> >>>> I'm using editconf and I need to select several groups at same time.
> >> How to
> >>>> do that?
> >>>>
> >>>> Thanks!
> >>>> Rita.
> >>>>
> >>>> --
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> >>>
> >>>
> >>>
> >>> --
> >>> Tsjerk A. Wassenaar, Ph.D.
> >>> --
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> >> The University of Dundee is a registered Scottish Charity, No: SC015096
> >
> >
> >
> > --
> > Catarina A. Carvalheda
> >
> > PhD Student
> > Computational Biology Division
> > SSE & SLS
> > University of Dundee
> > DD1 5EH, Dundee, Scotland, UK
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> The University of Dundee is a registered Scottish Charity, No: SC015096
>



-- 
Catarina A. Carvalheda

PhD Student
Computational Biology Division
SSE & SLS
University of Dundee
DD1 5EH, Dundee, Scotland, UK