Provided by: gromacs-data_2018.1-1_all bug


       gmx-do_dssp - 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  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

       Since  version 2.0.0, dssp is invoked with a syntax that differs from earlier versions. If
       you have an older version of dssp, use the -ver option to direct do_dssp to use the  older
       syntax.   By  default,  do_dssp uses the syntax introduced with version 2.0.0.  Even newer
       versions (which at the time of writing are not yet released) are assumed to have the  same
       syntax as 2.0.0.

       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

       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)
              Index file

       -map [<.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



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       2018, GROMACS development team