---
name: "gmx-do_dssp"
section: "1"
platform: "linux"
package: "gromacs-data"
version: "2022.5-2"
release: "Debian 12 (Bookworm)"
platforms: ["linux"]
url: "https://new.carta.tech/gmx-do_dssp"
---

# gmx-do\_dssp(1)

Assign secondary structure and calculate solvent accessible surface area

## 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)](/gmx/1.md)**

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

## COPYRIGHT

*2023, GROMACS development team*