[gmx-users] Help with editconf

[Rita Galvão]

:) yes, i have the complete system.. Obrigada Catarina!!!

Rita

No dia 17/12/2015, às 15:21, "Catarina A. Carvalheda dos Santos" <c.a.c.dossantos at dundee.ac.uk> escreveu:

> 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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>>>> Gromacs Users mailing list
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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
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> 
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