table of contents
g_helix(1) | GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c | g_helix(1) |
NAME¶
g_helix - calculates basic properties of alpha helicesSYNOPSIS¶
g_helix -s topol.tpr -n index.ndx -f traj.xtc -to gtraj.g87 -cz zconf.gro -co waver.gro -[no]h -[no]version -nice int -b time -e time -dt time -[no]w -r0 int -[no]q -[no]F -[no]db -prop enum -[no]ev -ahxstart int -ahxend intDESCRIPTION¶
g_helix computes all kinds of helix properties. First, the peptide is checked to find the longest helical part, as determined by hydrogen bonds and phi/psi angles. That bit is fitted to an ideal helix around the z-axis and centered around the origin. Then the following properties are computed:FILES¶
-s topol.tpr InputRun input file: tpr tpb tpa
Index file
Trajectory: xtc trr trj gro g96 pdb cpt
Gromos-87 ASCII trajectory format
Structure file: gro g96 pdb etc.
Structure file: gro g96 pdb etc.
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)
View output .xvg, .xpm, .eps and .pdb files
The first residue number in the sequence
Check at every step which part of the sequence is helical
Toggle fit to a perfect helix
Print debug info
Select property to weight eigenvectors with. WARNING experimental stuff: RAD, TWIST, RISE, LEN, NHX, DIP, RMS, CPHI, RMSA, PHI, PSI, HB3, HB4, HB5 or CD222
Write a new 'trajectory' file for ED
First residue in helix
Last residue in helix
SEE ALSO¶
gromacs(7)Mon 4 Apr 2011 |