g_do_dssp_d (1) - Linux Man Pages

g_do_dssp_d: assigns secondary structure and calculates solvent accessible surface area

NAME

do_dssp - assigns secondary structure and calculates solvent accessible surface area

VERSION 4.0.1

SYNOPSIS

do_dssp -f traj.xtc -s topol.tpr -n index.ndx -ssdump ssdump.dat -map ss.map -o ss.xpm -sc scount.xvg -a area.xpm -ta totarea.xvg -aa averarea.xvg -[no]h -nice int -b time -e time -dt time -tu enum -[no]w -[no]xvgr -sss string

DESCRIPTION

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. do_dssp assumes that the dssp executable is /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 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. 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 (A2) 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 g_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 g_chi. Together these two programs can be used to analyze dihedral properties as a function of secondary structure type.

FILES

-f traj.xtc Input
 Trajectory: xtc trr trj gro g96 pdb cpt 

-s topol.tpr Input
 Structure+mass(db): tpr tpb tpa gro g96 pdb 

-n index.ndx Input, Opt.
 Index file 

-ssdump ssdump.dat Output, Opt.
 Generic data file 

-map ss.map Input, Lib.
 File that maps matrix data to colors 

-o ss.xpm Output
 X PixMap compatible matrix file 

-sc scount.xvg Output
 xvgr/xmgr file 

-a area.xpm Output, Opt.
 X PixMap compatible matrix file 

-ta totarea.xvg Output, Opt.
 xvgr/xmgr file 

-aa averarea.xvg Output, Opt.
 xvgr/xmgr file 

OTHER OPTIONS

-[no]hno
 Print help info and quit

-nice int 19
 Set the nicelevel

-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 when t MOD dt first time (ps)

-tu enum ps
 Time unit:  ps fs ns us ms or  s

-[no]wno
 View output xvg, xpm, eps and pdb files

-[no]xvgryes
 Add specific codes (legends etc.) in the output xvg files for the xmgrace program

-sss string HEBT
 Secondary structures for structure count

SEE ALSO

gromacs(7)

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