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 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 setenv DSSP /opt/dssp/bin/dssp
26 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 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 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 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.
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54 Options to specify input files:
55 -f [<.xtc/.trr/…>] (traj.xtc)
57 Trajectory: xtc trr cpt gro g96 pdb tng
58 -s [<.tpr/.gro/…>] (topol.tpr)
60 Structure+mass(db): tpr gro g96 pdb brk ent
61 -n [<.ndx>] (index.ndx) (Optional)
63 Index file
64 -map [<.map>] (ss.map) (Library)
66 File that maps matrix data to colors
67 Options to specify output files:
69 -ssdump [<.dat>] (ssdump.dat) (Optional)
71 Generic data file
72 -o [<.xpm>] (ss.xpm)
74 X PixMap compatible matrix file
75 -sc [<.xvg>] (scount.xvg)
77 xvgr/xmgr file
78 -a [<.xpm>] (area.xpm) (Optional)
80 X PixMap compatible matrix file
81 -ta [<.xvg>] (totarea.xvg) (Optional)
83 xvgr/xmgr file
84 -aa [<.xvg>] (averarea.xvg) (Optional)
86 xvgr/xmgr file
87 Other options:
89 -b <time> (0)
91 Time of first frame to read from trajectory (default unit ps)
92 -e <time> (0)
94 Time of last frame to read from trajectory (default unit ps)
95 -dt <time> (0)
97 Only use frame when t MOD dt = first time (default unit ps)
98 -tu <enum> (ps)
100 Unit for time values: fs, ps, ns, us, ms, s
101 -[no]w (no)
103 View output .xvg, .xpm, .eps and .pdb files
104 -xvg <enum> (xmgrace)
106 xvg plot formatting: xmgrace, xmgr, none
107 -sss <string> (HEBT)
109 Secondary structures for structure count
110 -ver <int> (2)
112 DSSP major version. Syntax changed with version 2
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115 gmx(1)
116 More information about GROMACS is available at <‐
118 http://www.gromacs.org/>.
119
121 2019, GROMACS development team
1222019.4 Oct 02, 2019 GMX-DO_DSSP(1)