Provided by: gromacs-data_2022.2-1_all bug

NAME
       gmx-do_dssp - Assign secondary structure and calculate solvent accessible surface area


SYNOPSIS
          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>]


DESCRIPTION
       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
       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)
              Index file

       -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)
              xvgr/xmgr file

       -a [<.xpm>] (area.xpm) (Optional)
              X PixMap compatible matrix file

       -ta [<.xvg>] (totarea.xvg) (Optional)
              xvgr/xmgr file

       -aa [<.xvg>] (averarea.xvg) (Optional)
              xvgr/xmgr file

       Other options:

       -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.


SEE ALSO
       gmx(1)

       More information about GROMACS is available at <http://www.gromacs.org/>.


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       2022, GROMACS development team