1GMX-DO_DSSP(1)                      GROMACS                     GMX-DO_DSSP(1)
2
3
4

NAME

6       gmx-do_dssp - Assign secondary structure and calculate solvent accessi‐
7       ble surface area
8

SYNOPSIS

10          gmx do_dssp [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
11                      [-map [<.map>]] [-ssdump [<.dat>]] [-o [<.xpm>]]
12                      [-sc [<.xvg>]] [-a [<.xpm>]] [-ta [<.xvg>]]
13                      [-aa [<.xvg>]] [-b <time>] [-e <time>] [-dt <time>]
14                      [-tu <enum>] [-[no]w] [-xvg <enum>] [-sss <string>]
15                      [-ver <int>]
16

DESCRIPTION

18       gmx do_dssp reads a trajectory file and computes the  secondary  struc‐
19       ture  for  each time frame calling the dssp program. If you do not have
20       the dssp program,  get  it  from  http://swift.cmbi.ru.nl/gv/dssp.  gmx
21       do_dssp    assumes   that   the   dssp   executable   is   located   in
22       /usr/local/bin/dssp. If this is not the case, then you  should  set  an
23       environment variable DSSP pointing to the dssp executable, e.g.:
24
25       setenv DSSP /opt/dssp/bin/dssp
26
27       Since  version  2.0.0,  dssp is invoked with a syntax that differs from
28       earlier versions. If you have an older version of dssp,  use  the  -ver
29       option  to direct do_dssp to use the older syntax.  By default, do_dssp
30       uses the syntax introduced with version  2.0.0.   Even  newer  versions
31       (which at the time of writing are not yet released) are assumed to have
32       the same syntax as 2.0.0.
33
34       The structure assignment for each residue and time  is  written  to  an
35       .xpm  matrix file. This file can be visualized with for instance xv and
36       can be converted to postscript with xpm2ps.  Individual chains are sep‐
37       arated  by light grey lines in the .xpm and postscript files.  The num‐
38       ber of residues with each secondary structure type and the  total  sec‐
39       ondary structure (-sss) count as a function of time are also written to
40       file (-sc).
41
42       Solvent accessible surface (SAS) per residue can be calculated, both in
43       absolute  values  (A^2) and in fractions of the maximal accessible sur‐
44       face of a residue. The maximal accessible surface  is  defined  as  the
45       accessible  surface of a residue in a chain of glycines.  Note that the
46       program [gmx-sas] can also compute SAS and that is more efficient.
47
48       Finally, this program can dump the secondary  structure  in  a  special
49       file  ssdump.dat  for  usage in the program gmx chi. Together these two
50       programs can be used to analyze dihedral properties as  a  function  of
51       secondary structure type.
52

OPTIONS

54       Options to specify input files:
55
56       -f [<.xtc/.trr/…>] (traj.xtc)
57              Trajectory: xtc trr cpt gro g96 pdb tng
58
59       -s [<.tpr/.gro/…>] (topol.tpr)
60              Structure+mass(db): tpr gro g96 pdb brk ent
61
62       -n [<.ndx>] (index.ndx) (Optional)
63              Index file
64
65       -map [<.map>] (ss.map) (Library)
66              File that maps matrix data to colors
67
68       Options to specify output files:
69
70       -ssdump [<.dat>] (ssdump.dat) (Optional)
71              Generic data file
72
73       -o [<.xpm>] (ss.xpm)
74              X PixMap compatible matrix file
75
76       -sc [<.xvg>] (scount.xvg)
77              xvgr/xmgr file
78
79       -a [<.xpm>] (area.xpm) (Optional)
80              X PixMap compatible matrix file
81
82       -ta [<.xvg>] (totarea.xvg) (Optional)
83              xvgr/xmgr file
84
85       -aa [<.xvg>] (averarea.xvg) (Optional)
86              xvgr/xmgr file
87
88       Other options:
89
90       -b <time> (0)
91              Time of first frame to read from trajectory (default unit ps)
92
93       -e <time> (0)
94              Time of last frame to read from trajectory (default unit ps)
95
96       -dt <time> (0)
97              Only use frame when t MOD dt = first time (default unit ps)
98
99       -tu <enum> (ps)
100              Unit for time values: fs, ps, ns, us, ms, s
101
102       -[no]w (no)
103              View output .xvg, .xpm, .eps and .pdb files
104
105       -xvg <enum> (xmgrace)
106              xvg plot formatting: xmgrace, xmgr, none
107
108       -sss <string> (HEBT)
109              Secondary structures for structure count
110
111       -ver <int> (2)
112              DSSP major version. Syntax changed with version 2
113

SEE ALSO

115       gmx(1)
116
117       More     information    about    GROMACS    is    available    at    <‐
118       http://www.gromacs.org/>.
119
121       2019, GROMACS development team
122
123
124
125
1262019.4                           Oct 02, 2019                   GMX-DO_DSSP(1)
Impressum