make_ndx - makes index files
make_ndx -f conf.gro -n index.ndx -o index.ndx -[no]h -nice int -natoms
Index groups are necessary for almost every gromacs program. All these
programs can generate default index groups. You ONLY have to use
make_ndx when you need SPECIAL index groups. There is a default index
group for the whole system, 9 default index groups are generated for
proteins, a default index group is generated for every other residue
When no index file is supplied, also make_ndx will generate the default
groups. With the index editor you can select on atom, residue and
chain names and numbers. When a run input file is supplied you can
also select on atom type. You can use NOT, AND and OR, you can split
groups into chains, residues or atoms. You can delete and rename
The atom numbering in the editor and the index file starts at 1.
-f conf.gro Input, Opt.
Structure file: gro g96 pdb tpr tpb tpa
-n index.ndx Input, Opt., Mult.
-o index.ndx Output
Print help info and quit
-nice int 0
Set the nicelevel
-natoms int 0
set number of atoms (default: read from coordinate or index file)
More information about GROMACS is available at
Thu 16 Oct 2008 make_ndx(1)