[gmx-users] Selection syntax in make.ndx

[Catarina A. Carvalheda dos Santos]

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
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-request at gromacs.org.
> >>
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
>



-- 
Catarina A. Carvalheda

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