table of contents
do_dssp(1) | GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c | do_dssp(1) |
NAME¶
do_dssp - assigns secondary structure and calculates solvent accessible surface areaSYNOPSIS¶
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 -[no]version -nice int -b time -e time -dt time -tu enum -[no]w -xvg enum -sss stringDESCRIPTION¶
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 http://swift.cmbi.ru.nl/gv/dssp. 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.:FILES¶
-f traj.xtc InputTrajectory: xtc trr trj gro g96 pdb cpt
Structure+mass(db): tpr tpb tpa gro g96 pdb
Index file
Generic data file
File that maps matrix data to colors
X PixMap compatible matrix file
xvgr/xmgr file
X PixMap compatible matrix file
xvgr/xmgr file
xvgr/xmgr file
OTHER OPTIONS¶
-[no]hnoPrint help info and quit
Print version info and quit
Set the nicelevel
First frame (ps) to read from trajectory
Last frame (ps) to read from trajectory
Only use frame when t MOD dt = first time (ps)
Time unit: fs, ps, ns, us, ms or s
View output .xvg, .xpm, .eps and .pdb files
xvg plot formatting: xmgrace, xmgr or none
Secondary structures for structure count
SEE ALSO¶
gromacs(7)Mon 4 Apr 2011 |