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       do_dssp - assigns secondary structure and calculates solvent accessible
       surface area

       VERSION 4.0.1


       do_dssp -f traj.xtc -s topol.tpr -n index.ndx -ssdump  ssdump.dat  -map  -o  ss.xpm  -sc  scount.xvg  -a  area.xpm  -ta  totarea.xvg -aa
       averarea.xvg -[no]h -nice int -b time -e time -dt time -tu enum  -[no]w
       -[no]xvgr -sss string


       do_dssp  reads  a  trajectory file and computes the secondary structure
       for each time frame calling the dssp program. If you do  not  have  the
       dssp  program,  get  it.  do_dssp  assumes  that the dssp executable is
       /usr/local/bin/dssp. If this is not the case, then you  should  set  an
       environment variable  DSSP pointing to the dssp executable, e.g.:

        setenv DSSP /opt/dssp/bin/dssp

       The  structure  assignment  for each residue and time is written to an
       .xpm matrix file. This file can be visualized with for instance  xv and
       can  be  converted  to postscript with  xpm2ps.  The number of residues
       with each secondary structure type and the total secondary structure  (
       -sss) count as a function of time are also written to file ( -sc).

       Solvent accessible surface (SAS) per residue can be calculated, both in
       absolute values (A2) and in fractions of the maximal accessible surface
       of  a  residue.  The  maximal  accessible  surface  is  defined  as the
       accessible surface of a residue in a chain of glycines.   Note that the
       program  g_sas can also compute SAS and that is more efficient.

       Finally,  this  program  can  dump the secondary structure in a special
       file  ssdump.dat for usage in the program  g_chi.  Together  these  two
       programs  can  be  used to analyze dihedral properties as a function of
       secondary structure type.


       -f traj.xtc Input
        Trajectory: xtc trr trj gro g96 pdb cpt

       -s topol.tpr Input
        Structure+mass(db): tpr tpb tpa gro g96 pdb

       -n index.ndx Input, Opt.
        Index file

       -ssdump ssdump.dat Output, Opt.
        Generic data file

       -map Input, Lib.
        File that maps matrix data to colors

       -o ss.xpm Output
        X PixMap compatible matrix file

       -sc scount.xvg Output
        xvgr/xmgr file

       -a area.xpm Output, Opt.
        X PixMap compatible matrix file

       -ta totarea.xvg Output, Opt.
        xvgr/xmgr file

       -aa averarea.xvg Output, Opt.
        xvgr/xmgr file


        Print help info and quit

       -nice int 19
        Set the nicelevel

       -b time 0
        First frame (ps) to read from trajectory

       -e time 0
        Last frame (ps) to read from trajectory

       -dt time 0
        Only use frame when t MOD dt = first time (ps)

       -tu enum ps
        Time unit:  ps,  fs,  ns,  us,  ms or  s

        View output xvg, xpm, eps and pdb files

        Add specific codes (legends etc.) in the  output  xvg  files  for  the
       xmgrace program

       -sss string HEBT
        Secondary structures for structure count



       More      information     about     GROMACS     is     available     at

                                Thu 16 Oct 2008                     do_dssp(1)