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)