[gmx-users] Help with editconf

[Catarina A. Carvalheda dos Santos]

This is a very silly question, but I have to ask.
In your coordinates file (.gro or .pdb, option -f in the make_ndx tool) you
have the protein and the lipids, right?



On 17 December 2015 at 15:12, Catarina A. Carvalheda dos Santos <
c.a.c.dossantos at dundee.ac.uk> wrote:

> 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
>



-- 
Catarina A. Carvalheda

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