1do_dssp(1)                GROMACS suite, VERSION 4.5                do_dssp(1)
2
3
4

NAME

6       do_dssp - assigns secondary structure and calculates solvent accessible
7       surface area
8
9       VERSION 4.5
10

SYNOPSIS

12       do_dssp -f traj.xtc -s topol.tpr -n index.ndx -ssdump  ssdump.dat  -map
13       ss.map  -o  ss.xpm -sc scount.xvg -a area.xpm -ta totarea.xvg -aa aver‐
14       area.xvg -[no]h -[no]version -nice int -b time -e  time  -dt  time  -tu
15       enum -[no]w -xvg enum -sss string
16

DESCRIPTION

18       do_dssp  reads  a  trajectory file and computes the secondary structure
19       for each time frame calling the dssp program. If you do  not  have  the
20       dssp  program,  get  it.  do_dssp  assumes  that the dssp executable is
21       /usr/local/bin/dssp. If this is not the case, then you  should  set  an
22       environment variable  DSSP pointing to the dssp executable, e.g.:
23
24
25        setenv DSSP /opt/dssp/bin/dssp
26
27
28       The  structure  assignment  for each residue and time is written to an
29       .xpm matrix file. This file can be visualized with for instance  xv and
30       can  be  converted  to  postscript with  xpm2ps.  Individual chains are
31       separated by light grey lines in the xpm  and  postscript  files.   The
32       number  of  residues  with  each secondary structure type and the total
33       secondary structure ( -sss) count as a function of time are also  writ‐
34       ten to file ( -sc).
35
36
37       Solvent accessible surface (SAS) per residue can be calculated, both in
38       absolute values (A2) and in fractions of the maximal accessible surface
39       of a residue. The maximal accessible surface is defined as the accessi‐
40       ble surface of a residue in a chain of glycines.   Note that  the  pro‐
41       gram  g_sas can also compute SAS and that is more efficient.
42
43
44       Finally,  this  program  can  dump the secondary structure in a special
45       file  ssdump.dat for usage in the program  g_chi.  Together  these  two
46       programs  can  be  used to analyze dihedral properties as a function of
47       secondary structure type.
48

FILES

50       -f traj.xtc Input
51        Trajectory: xtc trr trj gro g96 pdb cpt
52
53       -s topol.tpr Input
54        Structure+mass(db): tpr tpb tpa gro g96 pdb
55
56       -n index.ndx Input, Opt.
57        Index file
58
59       -ssdump ssdump.dat Output, Opt.
60        Generic data file
61
62       -map ss.map Input, Lib.
63        File that maps matrix data to colors
64
65       -o ss.xpm Output
66        X PixMap compatible matrix file
67
68       -sc scount.xvg Output
69        xvgr/xmgr file
70
71       -a area.xpm Output, Opt.
72        X PixMap compatible matrix file
73
74       -ta totarea.xvg Output, Opt.
75        xvgr/xmgr file
76
77       -aa averarea.xvg Output, Opt.
78        xvgr/xmgr file
79
80

OTHER OPTIONS

82       -[no]hno
83        Print help info and quit
84
85       -[no]versionno
86        Print version info and quit
87
88       -nice int 19
89        Set the nicelevel
90
91       -b time 0
92        First frame (ps) to read from trajectory
93
94       -e time 0
95        Last frame (ps) to read from trajectory
96
97       -dt time 0
98        Only use frame when t MOD dt = first time (ps)
99
100       -tu enum ps
101        Time unit:  fs,  ps,  ns,  us,  ms or  s
102
103       -[no]wno
104        View output xvg, xpm, eps and pdb files
105
106       -xvg enum xmgrace
107        xvg plot formatting:  xmgrace,  xmgr or  none
108
109       -sss string HEBT
110        Secondary structures for structure count
111
112

SEE ALSO

114       gromacs(7)
115
116       More  information  about  GROMACS  is  available  at   <http://www.gro‐
117       macs.org/>.
118
119
120
121                                Thu 26 Aug 2010                     do_dssp(1)