NAME

       gmx-dssp - Calculate protein secondary structure via DSSP algorithm

SYNOPSIS

          gmx dssp [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
                   [-o [<.dat>]] [-b <time>] [-e <time>] [-dt <time>]
                   [-tu <enum>] [-fgroup <selection>] [-xvg <enum>]
                   [-[no]rmpbc] [-[no]pbc] [-sf <file>] [-selrpos <enum>]
                   [-seltype <enum>] [-sel <selection>] [-hmode <enum>]
                   [-[no]nb] [-cutoff <real>] [-[no]pihelix]
                   [-ppstretch <enum>]

DESCRIPTION

       gmx  dssp  allows  using  the  DSSP  algorithm  (namely, by detecting specific patterns of hydrogen bonds
       between amino acid residues) to determine the secondary structure of a protein.

       -hmode selects between using hydrogen atoms directly from the  structure  ("gromacs"  option)  and  using
       hydrogen pseudo-atoms based on C and O atom coordinates of previous residue ("dssp" option).

       -nb  allows  using  GROMACS  neighbor-search  method  to find residue pairs that may have a hydrogen bond
       instead of simply iterating over the residues among themselves.

       -cutoff is a real value that defines maximum distance from residue to its neighbor residue used  in  -nb.
       Minimum (and also recommended) value is 0.9.

       -pihelix changes pattern-search algorithm towards preference of pi-helices.

       -ppstretch  defines  stretch  value  of  polyproline-helices.  "shortened"  means stretch with size 2 and
       "default" means stretch with size 3.

       Note that gmx dssp currently is not capable of reproducing the  secondary  structure  of  proteins  whose
       structure  is  determined  by  methods  other  than X-ray crystallography (structures in .pdb format with
       incorrect values in the CRYST1 line) due to the incorrect cell size in such structures.

       Please note that the computation is always done in single precision,  regardless  of  the  precision  for
       which GROMACS was configured.

OPTIONS

       Options to specify input files:

       -f [<.xtc/.trr/...>] (traj.xtc) (Optional)
              Input trajectory or single configuration: xtc trr cpt gro g96 pdb tng

       -s [<.tpr/.gro/...>] (topol.tpr) (Optional)
              Input structure: tpr gro g96 pdb brk ent

       -n [<.ndx>] (index.ndx) (Optional)
              Extra index groups

       Options to specify output files:

       -o [<.dat>] (dssp.dat)
              Filename for DSSP output

       Other options:

       -b <time> (0)
              First frame (ps) to read from trajectory

       -e <time> (0)
              Last frame (ps) to read from trajectory

       -dt <time> (0)
              Only use frame if t MOD dt == first time (ps)

       -tu <enum> (ps)
              Unit for time values: fs, ps, ns, us, ms, s

       -fgroup <selection>
              Atoms stored in the trajectory file (if not set, assume first N atoms)

       -xvg <enum> (xmgrace)
              Plot formatting: xmgrace, xmgr, none

       -[no]rmpbc (yes)
              Make molecules whole for each frame

       -[no]pbc (yes)
              Use periodic boundary conditions for distance calculation

       -sf <file>
              Provide selections from files

       -selrpos <enum> (atom)
              Selection   reference   positions:   atom,  res_com,  res_cog,  mol_com,  mol_cog,  whole_res_com,
              whole_res_cog,   whole_mol_com,   whole_mol_cog,   part_res_com,    part_res_cog,    part_mol_com,
              part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog

       -seltype <enum> (atom)
              Default  selection  output  positions:  atom,  res_com,  res_cog, mol_com, mol_cog, whole_res_com,
              whole_res_cog,   whole_mol_com,   whole_mol_cog,   part_res_com,    part_res_cog,    part_mol_com,
              part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog

       -sel <selection>
              Group for DSSP

       -hmode <enum> (gromacs)
              Hydrogens pseudoatoms creating mode: gromacs, dssp

       -[no]nb (yes)
              Use GROMACS neighbor-search method

       -cutoff <real> (0.9)
              Distance from residue to its neighbor residue in neighbor search. Must be >= 0.9

       -[no]pihelix (no)
              Prefer Pi Helices

       -ppstretch <enum> (default)
              Stretch value for PP-helices: shortened, default

SEE ALSO

       gmx(1)

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

COPYRIGHT

       2023, GROMACS development team

2023.3                                            Oct 19, 2023                                       GMX-DSSP(1)