NAME

       do_dssp - assigns secondary structure and calculates solvent accessible surface area

       VERSION 4.6.5

SYNOPSIS

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

DESCRIPTION

        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 from http://swift.cmbi.ru.nl/gv/dssp.  do_dssp
       assumes that the dssp executable is located in  /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

       Since  version  2.0.0,  dssp  is invoked with a syntax that differs from earlier versions. If you have an
       older version of dssp, use the  -ver option to direct do_dssp to  use  the  older  syntax.   By  default,
       do_dssp uses the syntax introduced with version 2.0.0.  Even newer versions (which at the time of writing
       are not yet released) are assumed to have the same syntax as 2.0.0.

       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.  Individual chains  are
       separated  by  light  grey  lines  in  the   .xpm and postscript files.  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.

FILES

       -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 ss.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

OTHER OPTIONS

       -[no]hno
        Print help info and quit

       -[no]versionno
        Print version 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:  fs,  ps,  ns,  us,  ms or  s

       -[no]wno
        View output  .xvg,  .xpm,  .eps and  .pdb files

       -xvg enum xmgrace
        xvg plot formatting:  xmgrace,  xmgr or  none

       -sss string HEBT
        Secondary structures for structure count

       -ver int 2
        DSSP major version. Syntax changed with version 2

SEE ALSO

       gromacs(7)

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

                                                 Mon 2 Dec 2013                                       do_dssp(1)