Provided by: gromacs-data_4.6.5-1build1_all bug


       make_ndx - makes index files

       VERSION 4.6.5


       make_ndx -f conf.gro -n index.ndx -o index.ndx -[no]h -[no]version -nice int -natoms int


       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 for
       proteins, and a default index group is generated for every other residue name.

       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 groups.

       The atom numbering in the editor and the index file starts at 1.


       -f conf.gro Input, Opt.
        Structure file: gro g96 pdb tpr etc.

       -n index.ndx Input, Opt., Mult.
        Index file

       -o index.ndx Output
        Index file


        Print help info and quit

        Print version 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 <>.

                                          Mon 2 Dec 2013                              make_ndx(1)