gmx dssp#

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