1 .TH do_dssp 1 "Fri 19 Apr 2013" "" "GROMACS suite, VERSION 4.5.7"
3 do_dssp - assigns secondary structure and calculates solvent accessible surface area
9 .BI "\-s" " topol.tpr "
10 .BI "\-n" " index.ndx "
11 .BI "\-ssdump" " ssdump.dat "
12 .BI "\-map" " ss.map "
14 .BI "\-sc" " scount.xvg "
15 .BI "\-a" " area.xpm "
16 .BI "\-ta" " totarea.xvg "
17 .BI "\-aa" " averarea.xvg "
19 .BI "\-[no]version" ""
27 .BI "\-sss" " string "
30 \&reads a trajectory file and computes the secondary structure for
32 \&calling the dssp program. If you do not have the dssp program,
33 \&get it from http://swift.cmbi.ru.nl/gv/dssp. \fB do_dssp\fR assumes
34 \&that the dssp executable is located in
35 \&\fB /usr/local/bin/dssp\fR. If this is not the case, then you should
36 \&set an environment variable \fB DSSP\fR pointing to the dssp
40 \&\fB setenv DSSP /opt/dssp/bin/dssp\fR
43 \&The structure assignment for each residue and time is written to an
44 \&\fB .xpm\fR matrix file. This file can be visualized with for instance
45 \&\fB xv\fR and can be converted to postscript with \fB xpm2ps\fR.
46 \&Individual chains are separated by light grey lines in the \fB .xpm\fR and
48 \&The number of residues with each secondary structure type and the
49 \&total secondary structure (\fB \-sss\fR) count as a function of
50 \&time are also written to file (\fB \-sc\fR).
53 \&Solvent accessible surface (SAS) per residue can be calculated, both in
54 \&absolute values (A2) and in fractions of the maximal accessible
55 \&surface of a residue. The maximal accessible surface is defined as
56 \&the accessible surface of a residue in a chain of glycines.
57 \&\fB Note\fR that the program \fB g_sas\fR can also compute SAS
58 \&and that is more efficient.
61 \&Finally, this program can dump the secondary structure in a special file
62 \&\fB ssdump.dat\fR for usage in the program \fB g_chi\fR. Together
63 \&these two programs can be used to analyze dihedral properties as a
64 \&function of secondary structure type.
68 Trajectory: xtc trr trj gro g96 pdb cpt
70 .BI "\-s" " topol.tpr"
72 Structure+mass(db): tpr tpb tpa gro g96 pdb
74 .BI "\-n" " index.ndx"
78 .BI "\-ssdump" " ssdump.dat"
84 File that maps matrix data to colors
88 X PixMap compatible matrix file
90 .BI "\-sc" " scount.xvg"
96 X PixMap compatible matrix file
98 .BI "\-ta" " totarea.xvg"
102 .BI "\-aa" " averarea.xvg"
108 Print help info and quit
110 .BI "\-[no]version" "no "
111 Print version info and quit
113 .BI "\-nice" " int" " 19"
116 .BI "\-b" " time" " 0 "
117 First frame (ps) to read from trajectory
119 .BI "\-e" " time" " 0 "
120 Last frame (ps) to read from trajectory
122 .BI "\-dt" " time" " 0 "
123 Only use frame when t MOD dt = first time (ps)
125 .BI "\-tu" " enum" " ps"
126 Time unit: \fB fs\fR, \fB ps\fR, \fB ns\fR, \fB us\fR, \fB ms\fR or \fB s\fR
129 View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files
131 .BI "\-xvg" " enum" " xmgrace"
132 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR
134 .BI "\-sss" " string" " HEBT"
135 Secondary structures for structure count
140 More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.