gmx-do_dssp - Man Page
Assign secondary structure and calculate solvent accessible surface area
gmx do_dssp [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]] [-map [<.map>]] [-ssdump [<.dat>]] [-o [<.xpm>]] [-sc [<.xvg>]] [-a [<.xpm>]] [-ta [<.xvg>]] [-aa [<.xvg>]] [-b <time>] [-e <time>] [-dt <time>] [-tu <enum>] [-[no]w] [-xvg <enum>] [-sss <string>] [-ver <int>]
gmx do_dssp reads a trajectory file and computes the secondary structure for each time frame calling the dssp program. If you do not have the dssp program, get it from https://swift.cmbi.umcn.nl/gv/dssp. gmx do_dssp assumes that the dssp executable is located in /usr/local/bin/dssp. If this is not the case, then you should set an environment variable DSSP pointing to the dssp executable, e.g.:
setenv DSSP /opt/dssp/bin/dssp
The dssp program is invoked with a syntax that differs depending on version. Version 1, 2 and 4 are supported, and the correct invocation format can be selected using the -ver option. By default, do_dssp uses the syntax introduced with version 2.0.0. Newer versions might also have executable name mkdssp instead of dssp.
The structure assignment for each residue and time is written to an .xpm matrix file. This file can be visualized with for instance xv and can be converted to postscript with xpm2ps. Individual chains are separated by light grey lines in the .xpm and postscript files. The number of residues with each secondary structure type and the total secondary structure (-sss) count as a function of time are also written to file (-sc).
Solvent accessible surface (SAS) per residue can be calculated, both in absolute values (A^2) and in fractions of the maximal accessible surface of a residue. The maximal accessible surface is defined as the accessible surface of a residue in a chain of glycines. Note that the program [gmx-sas] can also compute SAS and that is more efficient.
Finally, this program can dump the secondary structure in a special file ssdump.dat for usage in the program gmx chi. Together these two programs can be used to analyze dihedral properties as a function of secondary structure type.
Options to specify input files:
- -f [<.xtc/.trr/...>] (traj.xtc)
Trajectory: xtc trr cpt gro g96 pdb tng
- -s [<.tpr/.gro/...>] (topol.tpr)
Structure+mass(db): tpr gro g96 pdb brk ent
- -n [<.ndx>] (index.ndx) (Optional)
- -map [<.map>] (ss.map) (Library)
File that maps matrix data to colors
Options to specify output files:
- -ssdump [<.dat>] (ssdump.dat) (Optional)
Generic data file
- -o [<.xpm>] (ss.xpm)
X PixMap compatible matrix file
- -sc [<.xvg>] (scount.xvg)
- -a [<.xpm>] (area.xpm) (Optional)
X PixMap compatible matrix file
- -ta [<.xvg>] (totarea.xvg) (Optional)
- -aa [<.xvg>] (averarea.xvg) (Optional)
- -b <time> (0)
Time of first frame to read from trajectory (default unit ps)
- -e <time> (0)
Time of last frame to read from trajectory (default unit ps)
- -dt <time> (0)
Only use frame when t MOD dt = first time (default unit ps)
- -tu <enum> (ps)
Unit for time values: fs, ps, ns, us, ms, s
- -[no]w (no)
View output .xvg, .xpm, .eps and .pdb files
- -xvg <enum> (xmgrace)
xvg plot formatting: xmgrace, xmgr, none
- -sss <string> (HEBT)
Secondary structures for structure count
- -ver <int> (2)
DSSP major version. Syntax changed with version 2 and 4.
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