1GMX-DO_DSSP(1) GROMACS GMX-DO_DSSP(1)
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6 gmx-do_dssp - Assign secondary structure and calculate solvent accessi‐
7 ble surface area
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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>]
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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 https://swift.cmbi.umcn.nl/gv/dssp. gmx
21 do_dssp assumes that the dssp executable is located in /usr/lo‐
22 cal/bin/dssp. If this is not the case, then you should set an environ‐
23 ment variable DSSP pointing to the dssp executable, e.g.:
24 setenv DSSP /opt/dssp/bin/dssp
26 The dssp program is invoked with a syntax that differs depending on
28 version. Version 1, 2 and 4 are supported, and the correct invocation
29 format can be selected using the -ver option. By default, do_dssp uses
30 the syntax introduced with version 2.0.0. Newer versions might also
31 have executable name mkdssp instead of dssp.
32 The structure assignment for each residue and time is written to an
34 .xpm matrix file. This file can be visualized with for instance xv and
35 can be converted to postscript with xpm2ps. Individual chains are sep‐
36 arated by light grey lines in the .xpm and postscript files. The num‐
37 ber of residues with each secondary structure type and the total sec‐
38 ondary structure (-sss) count as a function of time are also written to
39 file (-sc).
40 Solvent accessible surface (SAS) per residue can be calculated, both in
42 absolute values (A^2) and in fractions of the maximal accessible sur‐
43 face of a residue. The maximal accessible surface is defined as the ac‐
44 cessible surface of a residue in a chain of glycines. Note that the
45 program [gmx-sas] can also compute SAS and that is more efficient.
46 Finally, this program can dump the secondary structure in a special
48 file ssdump.dat for usage in the program gmx chi. Together these two
49 programs can be used to analyze dihedral properties as a function of
50 secondary structure type.
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53 Options to specify input files:
54 -f [<.xtc/.trr/...>] (traj.xtc)
56 Trajectory: xtc trr cpt gro g96 pdb tng
57 -s [<.tpr/.gro/...>] (topol.tpr)
59 Structure+mass(db): tpr gro g96 pdb brk ent
60 -n [<.ndx>] (index.ndx) (Optional)
62 Index file
63 -map [<.map>] (ss.map) (Library)
65 File that maps matrix data to colors
66 Options to specify output files:
68 -ssdump [<.dat>] (ssdump.dat) (Optional)
70 Generic data file
71 -o [<.xpm>] (ss.xpm)
73 X PixMap compatible matrix file
74 -sc [<.xvg>] (scount.xvg)
76 xvgr/xmgr file
77 -a [<.xpm>] (area.xpm) (Optional)
79 X PixMap compatible matrix file
80 -ta [<.xvg>] (totarea.xvg) (Optional)
82 xvgr/xmgr file
83 -aa [<.xvg>] (averarea.xvg) (Optional)
85 xvgr/xmgr file
86 Other options:
88 -b <time> (0)
90 Time of first frame to read from trajectory (default unit ps)
91 -e <time> (0)
93 Time of last frame to read from trajectory (default unit ps)
94 -dt <time> (0)
96 Only use frame when t MOD dt = first time (default unit ps)
97 -tu <enum> (ps)
99 Unit for time values: fs, ps, ns, us, ms, s
100 -[no]w (no)
102 View output .xvg, .xpm, .eps and .pdb files
103 -xvg <enum> (xmgrace)
105 xvg plot formatting: xmgrace, xmgr, none
106 -sss <string> (HEBT)
108 Secondary structures for structure count
109 -ver <int> (2)
111 DSSP major version. Syntax changed with version 2 and 4.
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114 gmx(1)
115 More information about GROMACS is available at <‐
117 http://www.gromacs.org/>.
118
120 2022, GROMACS development team
1212022.3 Sep 02, 2022 GMX-DO_DSSP(1)