gmx-do_dssp(1) GROMACS Manual gmx-do_dssp(1)NAMEgmx-do_dssp - Assign secondary structure and calculate solvent accessi‐
ble surface area
SYNOPSIS
gmx do_dssp [-f [<.xtc/.trr/...>]] [-s [<.tpr/.tpb/...>]]
[-n [<.ndx>]] [-ssdump [<.dat>]] [-map [<.map>]]
[-o [<.xpm>]] [-sc [<.xvg>]] [-a [<.xpm>]] [-ta [<.xvg>]]
[-aa [<.xvg>]] [-nice <int>] [-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 struc‐
ture 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 sepa‐
rated 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 accessi‐
ble 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 and output files:
-f [<.xtc/.trr/...>] (traj.xtc) (Input)
Trajectory: xtc trr cpt trj gro g96 pdb tng
-s [<.tpr/.tpb/...>] (topol.tpr) (Input)
Structure+mass(db): tpr tpb tpa gro g96 pdb brk ent
-n [<.ndx>] (index.ndx) (Input, Optional)
Index file
-ssdump [<.dat>] (ssdump.dat) (Output, Optional)
Generic data file
-map [<.map>] (ss.map) (Input, Library)
File that maps matrix data to colors
-o [<.xpm>] (ss.xpm) (Output)
X PixMap compatible matrix file
-sc [<.xvg>] (scount.xvg) (Output)
xvgr/xmgr file
-a [<.xpm>] (area.xpm) (Output, Optional)
X PixMap compatible matrix file
-ta [<.xvg>] (totarea.xvg) (Output, Optional)
xvgr/xmgr file
-aa [<.xvg>] (averarea.xvg) (Output, Optional)
xvgr/xmgr file
Other options:
-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, 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 ALSOgromacs(7)
More information about GROMACS is available at <http://www.gro‐
macs.org/>.
VERSION 5.0.6gmx-do_dssp(1)
