[gmx-users] Selection of multiple residues

[Bjoern Windshuegel]

Hi,

index files contain groups of atoms represented by their atom number. Just 
check an index file how it is constructed. By default, there are several 
groups (System, Protein, Protein-H, etc.).
So if you want to work with a range of residues (e.g. 1-300) just create a new 
group and copy the atom indices of those residues (1-xxxx) from another group 
into it (But carefully check from which existing group you are copying, 
depends on what you are interested). 

Best regards,

Björn




> "to select and copy the indices from an existing index-file to create a new
> group"
>
> I am sorry I did not understand the meaning of the above ? I will have the
> first atom number and the last atom number, and then ? How do I copy the
> indices ...
>
> On Fri, Feb 22, 2008 at 10:58 AM, Bjoern Windshuegel
> <bjorn.windshugel at uku.fi<mailto:bjorn.windshugel at uku.fi>> wrote: Hi,
>
> I assume you want to select a range of residues, not some scattered amino
> acids..
> So just check from your gro-file the atom numbers of begin and end of the
> region you need and use the information to select and copy the indices from
> an existing index-file to create a new group.
>
>
> Best regards,
>
> Björn
>
> > Hello,
> >
> > I want to select 300 residues out of my 1000 residue protein and make an
> > index out of it. make_ndx does not seem to have a simple method to do
> > this. These are all residues in the same chain. How does one do this ?
> >
> > Sincerely
> >
> > -Maria
> >
> > --
> > Maria G.
> > Technical University of Denmark
> > Copenhagen
>
> --
> Dr. Björn Windshügel
>
> Department of Pharmaceutical Chemistry
> University of Kuopio
> P.O. Box 1627
> 70211 Kuopio, FINLAND
>
> Email: bjorn.windshugel at uku.fi<mailto:bjorn.windshugel at uku.fi>
> Phone: (+358) 17 162463
> Fax:   (+358) 17 162456
> Web:  
> www.uku.fi/farmasia/fake/modelling/index.shtml<http://www.uku.fi/farmasia/f
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>
>
> --
> Maria G.
> Technical University of Denmark
> Copenhagen

-- 
Dr. Björn Windshügel

Department of Pharmaceutical Chemistry
University of Kuopio
P.O. Box 1627
70211 Kuopio, FINLAND

Email: bjorn.windshugel at uku.fi
Phone: (+358) 17 162463
Fax:   (+358) 17 162456
Web:   www.uku.fi/farmasia/fake/modelling/index.shtml