Provided by: gromacs-data_2018.1-1_all 
NAME
gmx-do_dssp - Assign secondary structure and calculate solvent accessible surface area
SYNOPSIS
gmx do_dssp [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
[-map [<.map>]] [-ssdump [<.dat>]] [-o [<.xpm>]]
[-sc [<.xvg>]] [-a [<.xpm>]] [-ta [<.xvg>]]
[-aa [<.xvg>]] [-b <time>] [-e <time>] [-dt <time>]
[-tu <enum>] [-[no]w] [-xvg <enum>] [-sss <string>]
[-ver <int>]
DESCRIPTION
gmx 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. gmx
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 (A^2) 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 [gmx-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 gmx chi. Together these two programs can be used to analyze dihedral properties as a function of
secondary structure type.
OPTIONS
Options to specify input files:
-f [<.xtc/.trr/…>] (traj.xtc)
Trajectory: xtc trr cpt gro g96 pdb tng
-s [<.tpr/.gro/…>] (topol.tpr)
Structure+mass(db): tpr gro g96 pdb brk ent
-n [<.ndx>] (index.ndx) (Optional)
Index file
-map [<.map>] (ss.map) (Library)
File that maps matrix data to colors
Options to specify output files:
-ssdump [<.dat>] (ssdump.dat) (Optional)
Generic data file
-o [<.xpm>] (ss.xpm)
X PixMap compatible matrix file
-sc [<.xvg>] (scount.xvg)
xvgr/xmgr file
-a [<.xpm>] (area.xpm) (Optional)
X PixMap compatible matrix file
-ta [<.xvg>] (totarea.xvg) (Optional)
xvgr/xmgr file
-aa [<.xvg>] (averarea.xvg) (Optional)
xvgr/xmgr file
Other options:
-b <time> (0)
Time of first frame to read from trajectory (default unit ps)
-e <time> (0)
Time of last frame to read from trajectory (default unit ps)
-dt <time> (0)
Only use frame when t MOD dt = first time (default unit ps)
-tu <enum> (ps)
Unit for time values: fs, ps, ns, us, ms, s
-[no]w (no)
View output .xvg, .xpm, .eps and .pdb files
-xvg <enum> (xmgrace)
xvg plot formatting: xmgrace, xmgr, none
-sss <string> (HEBT)
Secondary structures for structure count
-ver <int> (2)
DSSP major version. Syntax changed with version 2
SEE ALSO
gmx(1) More information about GROMACS is available at <http://www.gromacs.org/>.
COPYRIGHT
2018, GROMACS development team