[gmx-users] Selection of multiple residues
bjorn.windshugel at uku.fi
Fri Feb 22 12:23:30 CET 2008
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).
> "to select and copy the indices from an existing index-file to create a new
> 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
> 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,
> > 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
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> Maria G.
> Technical University of Denmark
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
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