[gmx-users] Selection syntax in make.ndx

[James Starlight]

Yep, thank so much!

It has already been 5 years of the usage of  Gromacs since finishing
of my PhD and still far away of understanding of all fundamentals !

James

2016-04-29 13:02 GMT+02:00 Catarina A. Carvalheda dos Santos
<c.a.c.dossantos at dundee.ac.uk>:
> James,
>
> Please try spending some time learning how to use GROMACS tools. Just
> because there's a mailing list it doesn't mean that you shouldn't try
> figuring things out by yourself beforehand.
> This is far too basic!
>
> 1. Protein
> 2. Chain A
>
>> 1 && ! 2
>
>
> On 29 April 2016 at 11:44, James Starlight <jmsstarlight at gmail.com> wrote:
>
>> Sory I did not find here the solution to my case
>>
>> 2016-04-29 12:40 GMT+02:00 Mark Abraham <mark.j.abraham at gmail.com>:
>> > Hi,
>> >
>> > Check out out gmx select. See
>> >
>> http://manual.gromacs.org/documentation/5.1/user-guide/cmdline.html#selection-syntax-and-usage
>> >
>> > Mark
>> >
>> >
>> >
>> > On Fri, Apr 29, 2016 at 12:37 PM James Starlight <jmsstarlight at gmail.com
>> >
>> > wrote:
>> >
>> >> Hi all!
>> >>
>> >> I am in charge with the analysis of multi-chain protein where each
>> >> chain defined as separate itp file in the topology.
>> >> My task is to make new ndx file for given tpr file defining chain A as
>> >> separate ndx group and all of the rest of the protein group but not
>> >> Chain A. Assuming to select chain A I just put Chain A (or
>> >> alternatively resid 1-100 for my case) how I can define selection
>> >> Protein and not Chain A or Pprotein and not resid 1-100 excluding
>> >> chain A or first 100 residues from the second selection?
>> >>
>> >>
>> >> Thanks for help!
>> >>
>> >> James
>> >> --
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>
>
>
> --
> Catarina A. Carvalheda
>
> PhD Student
> Computational Biology Division
> SLS & SSE
> University of Dundee
> DD1 5EH, Dundee, Scotland, UK
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