do_dssp(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c do_dssp(1)
NAME
do_dssp - assigns secondary structure and calculates solvent accessible surface area
VERSION 4.5.4-dev-20110404-bc5695c
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 aver-
area.xvg -[no]h -[no]version -nice int -b time -e time -dt time -tu enum -[no]w -xvg enum -sss string
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
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
SEE ALSO
gromacs(7)
More information about GROMACS is available at <http://www.gromacs.org/>.
Mon 4 Apr 2011 do_dssp(1)