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NAME

       make_ndx - makes index files

       VERSION 4.0.1

SYNOPSIS

       make_ndx -f conf.gro -n index.ndx -o index.ndx -[no]h -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 are generated for
       proteins, 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 tpb tpa

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

       -o index.ndx Output
        Index file

OTHER OPTIONS

       -[no]hno
        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)

SEE ALSO

       gromacs(7)

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

                                Thu 16 Oct 2008                    make_ndx(1)