NAME

       make_ndx - makes index files

       VERSION 4.6.5

SYNOPSIS

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

DESCRIPTION

       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.

FILES

       -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

OTHER OPTIONS

       -[no]hno
        Print help info and quit

       -[no]versionno
        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)

SEE ALSO

       gromacs(7)

       More information about GROMACS is available at <http://www.gromacs.org/>.

                                                 Mon 2 Dec 2013                                      make_ndx(1)