GMX-DO_DSSP(1)

📦
version 2022.5 · 2 versions
, in debian bookworm

💖 GMX-DO_DSSP(1) — like, the GROMACS one 💖

okay bestie, sit down, we're doing gmx-do_dssp today — it's a page from the GROMACS manual and it's literally the secondary-structure girlie. assigning secondary structure AND computing solvent accessible surface area?? she does it all 💅

✨ 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 🎀

so basically, gmx do_dssp reads a trajectory file and computes the secondary structure for each and every time frame, and it does that by calling the dssp program. iconic delegation honestly.

if you do not have the dssp program, bestie go get it from https://swift.cmbi.umcn.nl/gv/dssp 🫶

gmx do_dssp assumes the dssp executable lives at /usr/local/bin/dssp. if that's not the case (rude), you should set an environment variable DSSP pointing to the dssp executable, like:

setenv DSSP /opt/dssp/bin/dssp

the dssp program is invoked with a syntax that differs depending on version — versions 1, 2 and 4 are supported, and you pick the correct invocation format with the -ver option. by default, do_dssp uses the syntax introduced with version 2.0.0. newer versions might also have the executable name mkdssp instead of dssp — not me being extra, that's just how it is 🙈

the structure assignment for each residue and time gets 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, plus the total secondary structure (-sss) count as a function of time, also get written to file (-sc). slay ✨

solvent accessible surface (SAS) per residue can be calculated too — 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 it 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. the collab we deserved 💜

💅 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 👀

2023, GROMACS development team

no cap, that's the whole page. go compute some secondary structure bestie, you're the main character 🧚

this was the GROMACS manual, version 2022.5, dated Feb 03, 2023 — mwah, periodt 💋

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